Clash of the Phantoms
by Marcus S. Lazarus
Summary: -3rd in 'Phantom' trilogy- With his position in Atlantis now official, John must overcome his own perception of himself as old foes assume a new approach and his relationship with Elizabeth develops further
1. Out of the Mask

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: The third part in my 'Phantom of Atlantis' trilogy (Reading the first two stories in the series is highly recommended to ensure that you understand what's going on); for those returning fans, this take place about a month after the conclusion of 'Mystery of the Phantom', and as currently planned will cover the remaining key storylines in 'Atlantis', with some obvious and significant differences…

AN 2: Thanks are due to Elgin, who helped me refine a few details regarding the consequences of John's new role

Clash of the Phantoms

Sitting in his room as he adjusted his new suit- his complicated status meant that 'dress blues' weren't an official requirement, but General O'Neill had convinced him of the need to have something smart to wear in case a formal occasion or two came up- John was amazed that his life had gone through so many changes so quickly over the last few months.

On some level, it seemed like only yesterday that he'd still been acting as the Phantom the same way he'd done for years, hiding in the shadows and secret passages of Atlantis as he kept a careful eye on the city's inhabitants, and now he was in charge of the city's military contingent and essentially the second-in-command of the whole place. He'd been back in Atlantis for over a month now since his training on Earth had concluded, but it felt strange to have an actual room to himself rather than whatever safe location he could find in some of the city's maintenance tunnels.

With his presence in the city now public, Elizabeth had convinced him to deactivate some of the security protocols he'd established around certain parts of the city, arguing that they weren't needed now that he was there to explain _why _he'd sealed them away in the first place. Most of the rooms' contents were a surprise even to him- he'd recognised that the objects within the locked areas were dangerous when he'd found them, but he hadn't thought about most of them for so long he'd almost forgotten about them- but with the expedition's scientists to confirm his own assessment, they'd managed to dig up a few interesting pieces of technology.

The Ancients' temporary residence in the city had also opened up far more doors than even he had ever been able to access; he might have had access to several ZPMs, but he'd always restricted himself to one at a time when he was alone in the city, but the Ancients had been able to access far more buildings during their brief return. He'd had to stop McKay accidentally activating a DNA resequencing device they'd found in one area before the scientist did something serious to himself, and it had been a bit difficult to convince some of the staff not to touch that bizarre social experiment thing- it apparently resembled some kind of computer game back on Earth; he'd had to make a quick change and then take a team to the planet it was looking at to prove his claims- but once the first couple of teething troubles were out of the way even the most doubtful had accepted that he knew what he was talking about.

He'd even ensured that those new areas would stay open by providing the city with additional ZPMs from his own storage unit, as well as sending a few more back to Earth for use in the _Daedalus_ and other future ships, even if he'd taken care not to reveal just how many he had in his 'storehouse'; he wanted to keep some in reserve in case they were needed. He had also managed to neatly deflect attempts to convince him to reveal that information to the IOA and the rest of the Atlantis by claiming that he preferred to keep it quiet for reasons of security (The fact that the Wraith had already hacked the Atlantis database at least once made that far easier; he might have stopped the hack then, but it set a precedent that nobody wanted to risk repeating).

Of course, it wasn't as though there hadn't been some problems with his transition from his old role as mysterious vigilante to his new official status, but it was nothing for him to worry about. Most of the military personnel who disapproved of his presence had made their tastes clear by requesting to be transferred from Atlantis after the announcement was made, and while some of the science or medical team sometimes looked at him as though they were waiting for him to make some kind of mistake or expose his 'true intentions' (The memory of what General O'Neill had told him some people believed he'd been doing was hard to forget), in general everyone seemed willing to accept that he was only here to help, and the only thing that had changed since the old days was that he was officially allowed to do so. The new additions to his staff had also been generally welcoming. Captain Satterfield in particular had appreciated his insight into how the Wraith thought beyond a purely military perspective, and John admitted that he was coming to like her as well; her welcoming attitude made him feel like she was his younger sister in an odd way, appreciating his insight into life while still capable of handling herself.

Even without the larger problems, his appointment to the senior staff was currently somewhat problematic. Elizabeth had accepted him without hesitation, but Teyla and Ronon still looked at him as though they were waiting for the moment he'd revert to type and attack them; even if they accepted that he wasn't a traditional Wraithspawn, centuries of prejudice wasn't something that would be easily forgotten. McKay and Beckett were fairly neutral about his presence, accepting his new role even if they weren't completely comfortable with it, and Lorne and Satterfield were generally casual about it (He'd requested that they attend the meetings to provide him with the necessary military perspective and strategic intelligence he was still working on presenting, and so far they'd lived up to all his expectations).

Still, complicated personal dynamics aside, the Expedition's return to Pegasus had gone rather well. They maintained their tentative alliance with the Genii, the Athosians were willing to return to their previous roles working as local guides for recon teams, and their other major alliances had been easily re-established, particularly when their allies learned that the expedition was now officially working with the Phantom.

As far as the wider galaxy was concerned, nobody outside the expedition staff aside from a few trusted Athosians were aware that the Phantom and Atlantis's new military commander were the same person, but the knowledge that he was working with them officially was a definite boost to all relevant morale.

The Taranians had been particularly grateful to learn that contact between the Phantom and the city was now official, and their role in the daily operation of the _Orion _continued to be appreciated; Norena was essentially the ship's chief science officer, and Colonel Dixon had expressed nothing but satisfaction with her performance so far. With the recovery of the _Tria_'s database, the _Orion _crew and the expedition had managed to uncover some interesting details that it would have taken far longer to find if they were searching through Atlantis's own records.

The ships' databases hadn't provided anything particularly interesting yet- as an example, there were some brief descriptions of how to recharge the ZPMs, but there was nothing to indicate how to create them in the first place or how to assemble the necessary recharging equipment- but they had been able to direct them to a few interesting gate addresses that they wouldn't have arrived at on their own for some time.

The current destination was a planet on the outskirts of the Pegasus Galaxy, which had helped to protect it from attracting the attention of the Wraith. Unlike the expedition's less pleasant contact with Halcyon the previous year- one planet where John freely admitted that the expedition had been far better qualified to help than he had been; his status as a legend made it difficult for the Phantom to encourage social change- this world, known to its inhabitants as Rhean, had managed to develop a far more positive culture, based less around military conquest and more about improving their own world. The Ancient database from the _Tria _had identified the world as the sight of a former Ancient research outpost that had fallen victim to some kind of accident during the Wraith war that had infected most of the population with an unspecified disease, but had noted that the radiation that caused the disease would have died down by now.

When John and his new team had visited the relevant gate address, they'd learned that the planet had acquired an indigenous population that had set up a colony in most of the abandoned Ancient buildings at some point after the radiation had died down, using some of the information in the planet's database to improve their environment and ensure their safety from the Wraith.

While Rhean was far enough away from the heart of the galaxy to avoid attracting the majority of the Wraith forces in Pegasus, the Rheans were still aware of the dangers out in the wider universe, and were using the outpost's available resources to try and improve their daily lives before they tried to look further afield. The outpost had little to offer compared to Atlantis's resources, but they'd already managed to uncover some interesting terraforming systems, and had even worked out how to activate the outpost's defensive shield- a weaker version of the Atlantis shield but still fairly durable- along with a cloaking system.

Of course, the Rheans' limited population- virtually the planet's entire population lived around the outpost itself- meant that their study of the outpost had been highly publicised, with the result that Atlantis's contact with them had swiftly become a major cause for celebration on the planet as well as for the expedition. As the official announcement of the new alliance with the Rheans was the first big event that Atlantis had experienced since John Sheppard had become its military commander, it meant that his presence was required at the treaty signings and the party that was being held in their honour in the aftermath (Elizabeth was going to do most of the work, but it was still up to John to be there to supervise everything).

It might not be a completely leisurely outing, but as he finished adjusting his suit and left his room to join his team at the Stargate, John had to admit that he was kind of looking forward to this; he hadn't been to a party since before he arrived in Pegasus…

And the fact that he was going to get a chance to dance with Elizabeth was _not _the main reason for his enjoyment; the dance was just a… welcome bonus.

He'd accepted that Elizabeth would only ever see him as a friend and colleague; why couldn't he _get over it_…?

* * *

AN 3: Slow start, I know, but be patient; things will become more interesting after the next chapter…


	2. John Sheppard's First Night Out

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: This chapter proved tricky at times, but I hope it was worth it; we're coming up to my interpretation of one of my favourite episodes of 'Atlantis'…

Clash of the Phantoms

Walking alongside Elizabeth as the Atlantis team were guided to the main hall, John fought down the urge to scratch at his face. The make-up used to create his 'regular appearance' was very good at feigning the appearance of regular skin, but it still felt somewhat uncomfortable against his damaged face, made worse by his inability to scratch it in case he ruined his disguise…

Still, his own discomfort was a small price to pay compared to everything else that was going on right now. The treaty signing had gone as well as could be expected, Elizabeth and the Rhean leader only needing a few moments to clarify a few of the finer details, and they were currently being escorted further into the town's main hall in order to enjoy the subsequent celebration.

"Here we are," Mayor Coralin said, smiling as he indicated the central hall before them, the walls resembling Atlantis's usual architecture apart from some slight stains and wear and tear around the corners. "Our central hall; I apologise for its relative simplicity."

"Don't worry about it," Elizabeth said, smiling at them in understanding as she glanced around the room. The decorations added to the room were relatively sparse, consisting only of a few tapestries on the walls and some basic furniture in the corners, but the stage set up at one end of the hall and the band assembled there added an extra warmth to the hall that Atlantis had never quite managed to possess even after three years (John wouldn't consider the possibility that he'd contributed to that; he'd never intended to act like an oppressive force and had no doubt that Elizabeth would have told him if he was creating a bad impression). "We've dealt with the fine print; it's time to just have some fun."

"A sentiment that I am sure my people agree with just as much, Doctor Weir," Coralin said, smiling at her once more before he waved a hand at the band at the other end of the hall. The instruments they were playing didn't immediately resemble anything John was familiar with, but as they began playing the resulting rhythm was actually rather pleasant, creating a soothing atmosphere that felt intriguing rather than confusing due to the unfamiliar notes.

As the expedition members attending the treaty signing filed into the hall, John moved over to discreetly take up a position between the door and a window, to better assess the new arrivals. The fact that the hall was so full made John more and less comfortable at the same time; on the one hand, he wasn't used to crowds after spending so long alone in Atlantis, but on the other hand, he felt less conspicuous this way, even if he was here as a high-ranking member of the Atlantis expedition.

As well as the city's senior staff and some of Atlantis's more long-term residents, Colonel Dixon and some of the other senior staff for the _Orion _had decided to attend the party as well, but the _Orion _itself was remaining in orbit; it might be capable of landing, but it was easier to leave the ship in space rather than bring it into land. Glancing over, John was pleased to see Dixon sharing a dance with Norina Pero; the Taranian scientist had proven to be a quick study once given access to more advanced resources than what the Ancients had originally left on Taranis, and even the _Orion_'s Tau'ri crewmembers were comfortable regarding her as the ship's chief scientist, as well as the unofficial leader of the Taranian section of the crew.

Atlantis's connections in Pegasus were still fairly tentative aside from their contact with the Athosians, but with Atlantis now able to officially proclaim that they were allied with the Phantom, even the IOA had to admit that John's information was proving to be very helpful in terms of improving their relationship with their allies.

As the last of the attendees entered the hall, John allowed the music to wash over him as he turned to study the view through the nearby window. The night sky he witnessed was one of the most incredible he'd ever seen, a band of stars seemingly spreading out from the planet as the rest of the Pegasus Galaxy extended away from their current location, the stars standing out all the more brightly in the absence of other light sources in this part of space.

He enjoyed his life in Atlantis, but one thing John had missed about being able to travel through the Stargate during his time in hiding was the chance to see different stars like this…

"Shall we dance?"

John had been intending to turn the offer down when he initially turned around, but when he realised that Elizabeth was the one who had made the offer, he suddenly didn't know what to say apart from nodding politely at her and taking her hand as she led him to the dancefloor.

He didn't know the song, and his knowledge of any dance routine was limited, but as he moved across the dance floor with Elizabeth in his arms, standing slightly apart even as Elizabeth's hands met behind his neck and they swayed in time with the music, John had to fight down the urge to grin like an idiot at the sensation of her body so close to his.

Even if it never went further than this moment, even if she would never be closer to him than this for anything more than the occasion hug (And that was if he was lucky), these moments with her made all the hassle he'd endured back on Earth to 'qualify' for this position more than worth the effort. To know that she could see everything he was capable of and still trust him in such close proximity…

He'd never have the relationship he wanted, but he could accept what she was willing to give him if it led to moments like this.

"You're doing well," Elizabeth said, smiling as she stepped back to look approvingly at him.

"Just following your lead…" John said, shrugging dismissively as he resisted the urge to continue the dance; feeling her body pressed against his was more than he'd ever had a right to expect, but he couldn't afford to push his luck in case he gave away any more than he wanted to. "I'm just going to… scope this area out."

"Joh, we trust these people-"

"And I'm responsible for your security as part of my new position; I have to be sure," John said defensively. With that said, he stood back and walked over to the centre of the room, solemnly assessing his surroundings and the people dancing around as the party continued.

In truth, he was already fairly confident that the place would be secure from his earlier assessment, but if he didn't get away from Elizabeth, he wasn't sure what he'd do; being able to work with her on a regular basis was torture to his self-control…

Glancing around the hall to try and take his mind off that issue, John smiled as he saw McKay and Zelenka engaged in a heated discussion despite the best efforts of their dates ( John recognised Katie Brown from the botany department, but the identity of Zelenka's partner eluded him at the moment). They might have been working in different areas for a while when the expedition was sent back to Earth, but clearly some things didn't change no matter how much time people spent apart.

Satisfied that the two scientists were having no more trouble with each other than usual, John continued to assess the room. At one point, he noticed that Teyla was sharing a dance with a Japanese woman John didn't immediately recognise- he'd seen her working in the labs, but he couldn't place the name- but before he could start wondering what that said about either woman, the Athosian had handed the Japanese woman over to Ronan, the woman's brief appearance of panic being cut short as she and Ronan began to move across the floor. John guessed that the unfamiliar woman just needed some encouragement to open up after spending so long in the lab; the expedition weren't all workaholics, but there was only so much that they could do on Atlantis at the moment.

By contrast to the scientists, Satterfield was easily fitting in with the new environment, somehow managing to look particularly fetching despite wearing a standard dress uniform no more remarkable than those sported by the rest of the female military personnel present, having a different partner for each dance as the party unfolded. Even Elizabeth only had a couple of dances at a time, otherwise sitting off to the side discussing some of the finer details with other leaders, whether other department heads from Atlantis or some of the local leaders (And no, John was _not _jealous that other people were talking to her; so long as nobody tried to pull a Lucius, Elizabeth could make her own life…).

John was aware that sitting in a corner and drinking the local equivalent of beer might not be exactly sociable, but he was keeping himself available if anyone wanted to talk; he just didn't want to distract himself from his primary mission. Major Lorne, Colonel Dixon and everyone else had come a long way to be here and deserved the chance to experience what life in Pegasus had to offer; he was so familiar with some of the finer details by now that he didn't mind missing out on the simple things to ensure that others had a good time.

"Thank _god_…" a familiar voice said as someone slumped down in the chair beside John, clearly exhausted.

"Doctor Beckett?" John said, looking at his new companion in surprise, the man clearly sweating in his unusually formal suit. "What's wrong?"

"Just… well… the mayor's assistant," Beckett said, indicating a rather fetching young woman with dark hair wearing a form-fitting dark blue dress, standing at the hall's bar and looking at the doctor in a very seductive manner. "I mean, she was nice enough when we were talking earlier, but then we started dancing, and…"

"And it went wrong?" John asked. "What, did you step on her foot or something?"

"No, that's the thing; it was all fine, but I'm just…" Beckett said, voice trailing off as he looked awkwardly at the woman before he looked back at John. "I'm just not _used _to this… kind of attention…"

"Weren't you dating Laura Cadman before you went back to Earth?"

"Yeah, but it didn't really work out; probably something to do with us having our first kiss through Rodney," Beckett said, smiling briefly at the memory before he looked anxiously at the woman. "The point is, I'm just getting out of one relationship, and now-"

"Doctor Beckett, I've… not exactly been a social guy for the last few years; if you're looking for advice on what to do in this situation, I'm far from the best person to ask," John said, looking apologetically at the other man; he appreciated that the other man was trying to bond, but this was so far out of his experience that it was ridiculous to imagine anyone thinking that he could offer useful advice right now. "All I can say is that, if you like spending time with her… well, considering how hard it is to meet people here, anything's worth giving it a shot; worry about everything else later on."

"Oh," Beckett said, apparently realising that there was something deeper about that comment, but clearly recognising that this wasn't the time to press the issue. Nodding at John in understanding, he took a quick gulp of his drink and then turned back towards the woman, the two resuming their dance a few moments later. The doctor still appeared to be somewhat awkward around his partner, but at least he was giving her a chance; in a world this complicated, it was always good to find someone.

It was just too bad that his someone would never see him that way…

Wanting to avoid that thought, John turned and headed for the nearest exterior door, slipping out before anyone could see him; after spending the last two years stuck inside places, he needed to start spending more time out in the air before he started to get too used to it. Once he was sure that nobody would follow him, John settled into position as he stared upwards, the reassuring metal at his back and the vegetation spread out before him a welcome change from past trips he'd been on recently as he resumed his earlier contemplation of the night sky.

Back when he'd been training as the Phantom, he'd sometimes left Atlantis to take a break on other worlds, exploiting the fact that he was the only one who could dial Atlantis's gate at that time, but he'd always been restricted to uninhabited planets to limit the risk of being discovered- it wouldn't have done for anyone to find the legendary Phantom _training_-; as much as he'd appreciated the chance to relax, those trips had just reinforced how fundamentally alone he had been in this part of the galaxy. Every trip had always brought home just how alone he was on his chosen path, unable to spend too much time with anyone in case they saw what was under his mask or witnessed something that would make them question the legend he was trying to create around himself; he'd been the Phantom for so many years it was an effort to just be John Sheppard at times.

Elizabeth made it easier, of course- he'd spent so long letting down his guard when talking to her now-cremated future self that he associated her with the ability to relax- but there was only so much that she could do to help _him _when a whole city depended on her for leadership…

Right now, however, with the chance to rest on a world that had other people on it without worrying too much about how people would perceive him… the opportunity to see the sky and natural vegetation on a populated world… and being able to do it all when everyone else saw him as just one of the crowd from Atlantis, rather than revering him as 'the Phantom of the Ancestors' (A title that he was going to start discouraging as soon as he could after the 'Ancestors' had turned out to be complete dicks)…

He hadn't realised how much he'd missed those simple things until he'd been to Earth…

"Excuse me?" a voice said from behind him.

Turning around, John smiled politely at the young woman coming up behind him, wearing a long dark coat over her dress.

"Are you… all right?" the woman asked, looking uncertainly at him. "The party is-?"

"The party's fine; I just… wanted to catch my breath," John said, smiling reassuringly at her; he didn't think these people were easily offended, but it was better to be safe than sorry. "We haven't been to many of these things; it's a bit trickier closer to the galactic centre, you know…"

"Indeed," the woman said, smiling slightly at him. "Forgive me, but I had heard that a… Colonel Sumner was the military commander of Atlantis?"

"He moved on from the city," John said, going with the diplomatic explanation they'd come up with; Sumner's attitude at least ensured that he hadn't formed any particular bonds with any of the civilisations they'd encountered over the years, but it was better to be safe rather than sorry. "John Sheppard; I'm the expedition's new director of military operations. You are?"

"I am Ida," the woman said, before her eyes narrowed and her friendly expression vanished. "And your city's false Phantom killed my brother."

Even with his years of training as the Phantom, John was just slightly too slow to react (In hindsight, he'd blame it on the fact that he hadn't been expecting an attack here and he'd been drinking some of the planet's wine lately). Before he could get out of range, Ida had jammed something that felt like a taser into his chest, and he was falling backwards, consciousness fading, mouth open in a weak attempt to call for help…


	3. Awaken to Prison

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

When she glanced over and realised that John wasn't where he had been standing originally, Elizabeth wasn't sure how disappointed she should feel about his absence. She wanted him to open up to other people, of course- it was hardly fair of her to expect that she would remain his only real human contact now that he had an official position in Atlantis- but it was hard not to feel… 'jealous', was the best term that she could think of… that he was starting to talk to other people now.

Ever since John had returned to Atlantis as the new head of the city's military forces, their approach to searching for the city's secrets had been significantly altered. While John wasn't able to give them all the answers all of the time, with most rooms having been locked for the sake of security and caution rather than because he really _knew _that their contents were dangerous, he was still able to give them a fair amount of information about the city's secrets that they would have never known before, starting with him providing them with some of his surplus ZPMs to bring the city up to full power and progressing from there. While some members of the IOA had objected to John not disclosing the location of his ZPM storehouse, John had neatly deflected their arguments by pointing out the benefits of long-term secrecy in this situation, and nobody had been able to legitimately object to his argument that keeping the ZPMs' location secret would keep them much safer.

It was still too early to offer a definite opinion, but she had to admit that so far operations in Atlantis had been far smoother than they had been before. With John making a genuine effort to connect with his new staff as opposed to Sumner's professional detachment, the new recruits were complimenting the comfortable nature of Atlantis, even if a few of the returning military staff had expressed some uncertainty about what he had done in his private time in the previous two years. Satterfield in particular seemed to have developed a sibling-esque bond with John, treating him warmly without any sign that she was interested in more or judging him for his past.

She just wished that she could _feel _as good about that as she did; it was completely irrational to feel that jealous about the idea of John having more friends than her…

When she looked up and saw that John had vanished from the area where he had been standing earlier, she initially dismissed it as nothing; it was a big hall and John had a lot to deal with in his new role, so he was naturally trying to take in everything. It was only when she looked around the hall a few moments later and still couldn't see John that she began to get anxious. She had mixed feelings about John's protective nature at times- it sometimes seemed as though he felt that she couldn't be trusted to take care of herself- but she knew that he took his responsibilities seriously even before they became part of his official job; he wouldn't leave her at something this public on only his first trip away from Atlantis.

Glancing around to make sure none of the Rheans were paying too much attention to her, Elizabeth moved off to a corner of the room and sat down, conspicuously taking a drink and toying with it while waiting for other members of the expedition to pay attention to her. Eventually, McKay and Carson moved over to join her at the table, the two doctors looking uncertainly at her as they sat down.

"Something wrong?" Carson asked.

"John's missing," Elizabeth said.

"Missing?" McKay repeated. "It's a big hall with a lot of people in it-"

"I know what John looks like, Rodney; I would have seen him," Elizabeth said firmly; she couldn't fully explain how she could be so certain of that, even to herself, but she knew that she was telling the truth. "If he's not here, where he could be?"

"Well, I know I talked to him a little while ago; he was just… there…" Carson said, indicating the same area where she had last seen John; at least she could be sure that John hadn't gone far if he was sticking around one area.

"Have either of you seen him since then?" she asked, glancing around the area in case she'd missed something; she was still adjusting to seeing John's 'real' face after so long recognising him only by the mask- in a strange way, she saw his new face as just a variation on the original mask- but she felt sure that she would have seen him by now…

Her eyes fell on a door near where John had last been seen, and she quickly got up from her chair to take a closer look. Hurrying through the crowd, she managed to sidestep most of the Rheans' attempts to talk to her while the two doctors followed behind her, only briefly registering Teyla and Ronon coming over to join her as she walked before she reached the door.

When she opened the door and saw nothing, she briefly hoped that she'd made a mistake, but that hope was dashed when she saw marks on the ground; she might not be a professional tracker, but those were definitely drag marks. Turning around, she was saved from asking for help when Ronon crouched down to examine the marks more closely.

"What is it?" she asked the former Runner.

"Something was dragged away from here," Ronon said, taking a moment to more thoroughly assess the marks before he looked back at her. "Something the size of a human male… who was out here?"

"John," she replied, knowing that Ronon would know who she was talking about; the Pegasus natives might have come to recognise that certain names were more common than others back on Earth, but there was only one 'John' she'd identify by that name alone.

To Ronon's credit, despite his obvious discomfort with the man who had once just been the Phantom, he simply nodded at that information before he turned his attention back to the ground. Crouching down, he held out one hand to halt the others from moving forward as he ran his fingers across the upturned dust before him, until he picked something up.

"This look familiar?" the Runner asked, as he handed Elizabeth a small piece of something she recognised immediately.

She hadn't seen many details of John's 'disguise' beyond the 'before' and 'after' images, but she was fairly certain that nobody else at this party would need to be wearing this kind of false skin, and John would never remove it on his own outside of Atlantis, which meant that _something _had gone wrong.

"We need to move quickly," she said, looking urgently at the group around her. "Ronon, Teyla, get to the gate as fast as you can; it's the only way off-planet, and if someone took John, it's possible that they haven't managed to move on yet."

"Done," Ronon said, before he turned and ran towards the courtyard where this planet's Stargate was located, followed closely by Teyla. With that issue dealt with, Elizabeth turned and marched back into the hall with Beckett and McKay, taking a moment to beckon Major Lorne over to join her before heading for the mayor.

"Doctor Weir?" the mayor said, looking at her in surprise. "What is-?"

"My chief military officer has just gone missing, and I have reason to believe that he has been abducted," Elizabeth said, looking firmly at the other man, the new major's presence behind her giving her a degree of confidence as she made her statement. "Aside from everyone here, who else knew that we were coming?"

"Only a few of our mutual trading partners," the mayor replied; his shocked reaction to the news at least confirmed that he hadn't been expecting this news, but she had to assume that he had some idea of who could have been this even if he hadn't planned for it. "The Genii in particular seemed interested; I believe that-"

"That's it," Major Lorne said, looking firmly over at Elizabeth. "It's the Genii."

"You believe that the Genii have captured your military leader?" the mayor said, looking at Major Lorne in surprise. "I understood you were allies-"

"We are _now_, but back when we first met, there were… difficulties," Elizabeth explained, fighting down her initial discomfort as she looked at her local counterpart. "I have no reason to believe that Ladon Radim would have done something like this, but there are… other factions among the Genii who wouldn't be as forgiving."

She didn't like to consider the possibility that Ladon could have betrayed them, but John had killed nearly sixty of their people during their attempt to take Atlantis. Ladon might be willing to forgive that as a past grievance, but that wouldn't stop some people from wanting to get revenge now…

She reminded herself that none of the Genii could know that John Sheppard was also the Phantom who had killed so many of their people during that last raid, but that could only give her so much comfort; even if they didn't recognise him, once they got past that make-up, he was going to be in serious trouble.

* * *

"Damnit…" John muttered, shaking his head in frustration as he opened his eyes. "Chloroform… who the hell _does _that to people any more?"

As he turned his head and realised that he was sitting in a cell, he cursed in frustration at his situation, only to realise that things were even worse when he felt the breeze against his damaged skin.

Whatever had happened to him, his current captors had removed his disguise, which meant that he was now _extremely _vulnerable and dealing with people who probably saw him as a feral beast who'd tear them apart at the slightest provocation…

"Hello?" he called out as he walked over to the cell door, not holding out much hope of a response but stuck for any alternatives. "Anyone there?"

"You're wasting your breath," a voice said. Glancing in the direction of the voice, John saw a small barred window in the wall, leading to a heavily-shadowed room that was almost certainly another cell.

"Didn't know I had company here," John noted, walking over to the cell.

"There is no escape," the voice said.

"There's no _intended _escape; that's not the same thing," John corrected, looking through the window to try and see his cellmate. "I know I probably look like something that should be in a stronger cage, but I'm not… y'know, a Wraithspawn…"

"I know," the voice said.

"You do?" John said in surprise. "How?"

"You were unconscious for too long and were too calm upon awakening," the voice replied. "A Wraithspawn would have awoken earlier and attempted to escape by breaking down the doors."

"Ah," John said, deciding to chalk that discovery up as a win and take it from there. "Good to know that _someone _has some sense here…"

"You doubt our captors will know the difference?" the voice asked.

"Let's just say they already have more reasons to dislike me than even they know of; the face probably just makes it easier for them to hate me," John elaborated, straining his eyes to see something in the gloom; he'd grown too used to the additional vision features of his mask. "How long have you been down here?"

"Many years," the voice said solemnly, accompanied by a clanking sound that made John think of chains.

"How many years?" he asked. "Five? Ten?"

"It no longer matters," the prisoner said solemnly.

"That long, huh?" John noted, trying not to feel too apprehensive at the thought that this prison was that good; it wasn't like many places in the galaxy had Atlantis's resources, after all. "What did you do to get here?"

"I merely allowed myself to be captured alive," the voice replied.

"Same here," John said, turning his attention back to the cell around him; with only his new dress uniform, he lacked most of the weapons he was used to packing in enemy territory, but at least he had some external options this time around. "Look, I'm sure that my people are looking for me; when they find me, we can-"

He was interrupted when a door opened and guards walked in, one of them walking up to his cell door and aiming a gun through it while another one opened the cell.

"Don't move," the man said, in a loud, clear voice that John would have normally associated with someone trying to tame a dangerous animal. "Stay still. Do nothing."

Under other circumstances, John might have made a joke, but with the guard clearly operating on a hair trigger and a large gun pointing at him, all he could do was raise his arms and wait as the other guard walked into the room, attaching handcuffs to his wrists as he was made to place them behind his back.

As he was marched out of the cell, he wondered if he should be more or less concerned about the fact that these people obviously thought he was some deranged animal rather than a self-trained soldier; he might be able to outsmart them if they were underestimating him, but it also meant that they would be keeping a _really _careful eye on him…


	4. The First Feeding

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

As he was marched into a different room and forced into a chair with manacles attached to the arms and legs, John took care to remain tensed as though he was about to spring into action; he was going to be sore later on from maintaining this posture, but at least this way he could give the impression that he was the feral animal waiting to pounce that they were expecting.

"So," Kolya said, as the Genii commander walked over to look at him, "now Atlantis employs Wraithspawn as leaders?"

"I know how to hit the Wraith hard," John replied, taking care to keep his responses brief; he wasn't going to act like a mindless animal, but he had to give the impression of being very blunt if he wanted these guys to treat him like a conventional Wraithspawn. "It works for both of us."

"I see," Kolya said, his gaze hard before he shrugged. "In any case, what Atlantis does is not important to me now."

"And what _is _important to you?" John asked.

"All you need to know is that you will be returned to your city once I have achieved my goal," Kolya said. "That should be enough for you."

John couldn't risk asking more questions without attracting too much attention to what he really was, but he was already fairly sure that things weren't going to be as smooth as Kolya was implying.

The only positive thing right now was that at least Kolya hadn't realised who John really was; he could only imagine what the bastard would do to him if he knew that John was the Phantom who'd stopped him taking Atlantis…

* * *

Returned to Atlantis and back in her usual attire, Elizabeth wasn't sure if she should consider the current situation good or bad. Ronon and Teyla had reached the Stargate just in time to see people in what looked like Genii uniforms carry an unconscious form that was most likely John through the Stargate, but the gate had shut down before the two of them could get close enough to confirm that assessment or see what chevrons had been dialled, which meant that they were restricted to randomly checking the last fifty addresses dialled by that Stargate in no particular order.

Making contact with the Genii to discuss this turn of events had been awkward, but at least Ladon Radim appeared to be being honest when he claimed to have had no idea that anyone was trying to capture any member of the Atlantis expedition; they had too few useful allies in Pegasus to start doubting them now. She had calmed Ronan down when he had attempted to threaten Ladon to find out what he knew- Ronan might be uncomfortable about John's face, but he took his role in Atlantis seriously enough- but Ladon had only been able to tell them that the codes they'd given to the Genii had been stolen a while back without providing any definite suspects. Elizabeth had accepted the argument that he had come here with no ulterior intentions, putting himself completely in their hands despite the risks, but she had been forced to quickly talk Ronan down before he did anything they couldn't take back later. She had just been talking with Ladon in her office when the sound of the Stargate dialling was followed by an unscheduled offworld activation alert, prompting the two of them to hurry into the control room.

"Identification code?" she asked as she looked urgently at McKay, hoping against hope that John had made an escape on his own.

"None, but we're receiving an analogue video signal," McKay replied.

"Bring it up," Elizabeth said.

As the image of Commander Acastus Kolya appeared on the wallscreen, Elizabeth fought down the urge to shudder; the last time that man had been in Atlantis, he'd pushed John into acts of brutality that still made her shiver when she thought about them, and that was before she considered what he'd almost done to her. The order to establish the video link he was looking for was issued almost automatically as Teyla clarified Kolya's identity for Ronon; the timing of events was too great for this to be a coincidence.

"This is Doctor Weir," she said, resisting the urge to vent her rage.

"_Good_," Kolya said with his usual sickening arrogance. "_I wanted to be sure that you were there to see this_."

That cryptic comment was explained as he stepped aside to reveal John trapped in a chair behind him, a white scarf tied over his mouth and his damaged face clearly visible.

"What have you done to him?" McKay asked.

"_Nothing… which is less than I should do, considering what he is_," Kolya said, now glaring at the screen. "_Does your blasphemy know no bounds, Doctor Weir? To have a false Phantom is one thing, but to give positions of authority to _Wraithspawn-"

"You didn't call us to criticise our methods, Commander," Elizabeth interjected, even as she privately noted that at least Kolya didn't know that he could potentially kill two birds with one stone right now; he clearly didn't know that John _was _the 'false' Phantom he was talking about, so at least he had no reason to inflict a more personal revenge on him. "What do you want?"

"_I wish to make a trade_," Kolya replied.

"Before we continue this conversation another second, I want to speak _with_ John Sheppard," Elizabeth interjected.

"_Be my guest_," Kolya said, stepping back and removing the scarf from John's face with a mocking grin.

"_Give him_ nothing," John said firmly, staring at the camera in his usual firm manner.

"_That's all you have to say_?" Kolya said, smirking at John as he indicated for his guards to put the gag back on before turning his attention back to the screen. "_Then again, I suppose I could expect nothing more from a Wraithspawn_…"

"What are your terms, Kolya?" Elizabeth asked; she didn't want to discuss what John appeared to be any more than she had to.

"_I have heard the familiar voices of yourself and Doctor McKay, but there is one person I know is there who has yet to speak_," Kolya said, standing in front of John once again. "_Ladon Radim is with you, is he not_?"

"Why would Ladon be here?" Elizabeth asked.

"_Well, to preserve his precious alliance with you, Doctor, so that the Genii might remain in the favour of Atlantis_," Kolya replied casually. "_My sources have already confirmed this, so there's no point in denying the fact. Turn him over to me, and your pet Wraithspawn will be released immediately_."

"What makes you so sure we want him back?" Ronon asked. Elizabeth shot a frustrated glare over at Ronon, but she didn't dare to say anything; right now, she was fairly sure that Kolya wasn't receiving a return image from their end, but he would hear anything she had to say.

"_He might be a Wraithspawn, but you have already shown that you are willing to make… unconventional decisions_," Kolya said; judging by the sneer on his face, he still believed that they had used a fake Phantom to avert his takeover of Atlantis during their first encounter. "_I dislike repeating myself, but I will do so; in exchange for this man, I wish to receive Ladon Radim_."

"I'll need time to consider your offer," Elizabeth said, keeping her tone cold while looking over at Ladon to try and assure him that she wasn't genuinely thinking about taking the deal…

"_Allow me to help expedite your decision_," Kolya said, turning around to move the camera towards a door at the back of the room. For a moment, Elizabeth wondered what was going on, but when two guards appeared dragging a very unkempt-looking Wraith, with a shackle around its feeding hand hand and moving far more slowly than a healthy creature should, she couldn't restrain a gasp of horror.

"You-you've never even _met _John before!" McKay protested. "Why are you doing this? He doesn't deserve that!"

"_Let's be clear, Doctor McKay; no-one deserves this_," Kolya said coldly.

"Don't do this," Elizabeth said, as the guards removed the shackle on the Wraith's right hand.

"Don't do it."

"_The choice is yours, Doctor Weir_," Kolya said. "_Do we have an arrangement_?"

Elizabeth could only stare in silence as Kolya had the Wraith's hand placed against John's chest and began to feed, John throwing back his head in a manner that made his pain clear.

As much as it killed her to do this, John had spent years placing Atlantis ahead of himself; no matter how much she wanted to save him, she couldn't give any sign of weakness to men like Kolya in case they came back to try and get more through the same method.

Tightening her grip on the console in front of her, Elizabeth fought not to scream in rage as the Wraith was driven back from John with a cattle prod, hints of grey at his temples, pain on his face and a bleeding wound on the front of his chest…

"You just crossed a line, Kolya," she said, glaring coldly at the Genii commander.

"_We've found that a minimum of three hours between feeding sessions is crucial to ensure the body has sufficient time to recover from the trauma_," Kolya said; right now, Elizabeth wished that the screen was two-way so that she could make her contempt clear. "_That's the time you have to decide. Three hours_."

As the transmission came to an end, Elizabeth checked her watch, already planning how long they would have to find where Kolya was before John was subjected to that treatment again.

Things were bad enough when the Genii and that Wraith thought that they were just dealing with another member of Atlantis; how would any of them react to the discovery that they were dealing with the Phantom of Atlantis who'd defeated Kolya's attempt to take the city?

* * *

As he regained consciousness in his cell, John cursed his bad fortune.

He'd spent years managing to avoid being captured by the Wraith when he was engaging in battle with them in full Phantom regalia, working on his own with no hope of back-up, assistance, or treatment if things went wrong, and here he was, barely a month into his new role in Atlantis, and he'd been captured by a git and fed to a Wraith?

He didn't think that Atlantis had weakened his edge or anything like that, and he wouldn't trade his ability to talk freely with Elizabeth for anything, but this whole situation was so frustrating…

"They called you John Sheppard?" his fellow prisoner said from the next cell.

"Yeah," John said briefly. "That's my name. Pleased to meet you."

"You're in pain," the voice noted.

"Well, I just got fed on by a Wraith, what do you think?" John countered; at least now he didn't have to worry about maintaining the Phantom's appearance of strength in the face of adversity.

"I would not know," the other man said.

"Hopefully, you'll never have to find out," John said, groaning as he tried to straighten out; he felt like his bones had become suddenly stiff, most likely because of how much he'd aged since that thing fed from him. "I didn't think anything could hurt that much."

"You're still alive," the voice said.

"For the moment, but who knows how many years that thing took from my life?" John noted; the aging aspect of the Wraith feeding was one thing he was trying not to think about, but he had to at least acknowledge that he'd be slower than before once he got out of this. "I'll tell you this; if Kolya's men hadn't have pulled that damned thing off, I'd be dust in a suit."

"Do you blame the Wraith or the master?" the Wraith asked.

"Master?" John repeated, looking at the door between their cells in sudden suspicion.

Now that the voice had brought it up, he _had _given the issue of the Wraith feeding some thought over time; if nothing else, the Wraith mostly seemed to feed just because they needed to eat rather than out of any kind of sadistic desire to see humans die, even if a few took more pleasure in it than others. He knew that some Hives had formed a sort of alliance with various worlds; even if the humans were always the underdog in those relationships, planets such as Olesia showed that the Wraith could be open to negotiation if the right deal was offered, so they weren't just animals.

"I guess…" he said, still turning over his response as he gave it, "it would depend… on what the Wraith felt about it…"

"For the Wraith, hunger burns like a fire inside," the voice in the other cell said solemnly, shifting position slightly to reveal long, unkempt hair. "If you found yourself burning alive, would you settle for just one drop of water… or would you take more?"

"Good point," John said, deciding to avoid saying anything that might inspire more conflict; even if he disagreed with the decision to feed on humans, if he was right about the identity of his cellmate, the last thing he wanted was to provoke the guy…

Whatever John might feel about the Wraith normally, Kolya was the real problem right now; when he heard that kind of description of the hunger, and thought about what the person in the other cell must have gone through, the Wraith was basically just another victim, even if it was being used to torture him.

"So," he said, looking grimly at the creature in the next cell, "your hunger aside… no hard feelings, right?"

"I do what I must to survive," the Wraith said grimly, emerging from the shadows of his cell to reveal that his theory was correct. "I took barely more than a few years from you, and even the strength I gained from that is already fading."

"Yeah, we're both being tortured here, I get that; what matters is what we're going to _do _about it," John said, looking firmly at the creature he had fought for so many years.

"What we are going to do about it?" the Wraith repeated, looking at John in an almost quizzical manner.

"I've got people coming to look for me, but I'd rather not wait around any more than I have to," John clarified, as he looked at the creature. "We can spend our time complaining about the fact that we're both going through a lot of crap right now, or we can get out; I don't know about you, but I know what I want to try."

"There is no escape-" the Wraith began.

"Because you only had one man when you were trying to get out," John clarified. "Right now, there's two of us; has to be better odds, right?"

He couldn't believe that he was even attempting this, but even if Michael had stabbed him in the back, right now, the Wraith had no reason to see him as anything more than another victim of their captors; that had to count for _something_…


	5. Breaking Out with the Wraith

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

Even after talking with Ladon about what had happened to Kolya's reputation among the Genii following his failed conquest of Atlantis, Elizabeth couldn't find it in herself to pity him. She might be prejudiced because he'd tried to take her city and killed some of her people, but in her book, any man willing to go that far in the name of his own reputation against people who hadn't attacked them first didn't deserve to be in a position of authority over anyone, and his 'demotion' was thoroughly deserved.

Admittedly, she agreed with Ladon's opinion that Cowen and Kolya wouldn't have been suitable leaders for the Genii, even if she had some doubts about whether Ladon was the best choice or simply the best of bad choices, but she hadn't come to the Pegasus Galaxy to stage social coups; it wasn't her place to decide who should be in charge, but she would work with the current leader if he was willing to do the same. With Kolya targeting Ladon in particular, and Elizabeth having no reason to trust Kolya over Ladon, she was forced to accept the current status quo and hope that she wasn't misjudging him- he had been honest so far, even if she couldn't guarantee that would last- but the sooner she had John back in Atlantis, the better. Turning Ladon over might be the most immediate solution, but she wasn't going to betray someone who'd primarily acted to help them in favour of the man who'd tried to kill them once already; they had to find Kolya's base before things took a turn for the worse. Ladon had been able to give them a better idea where to look by studying their pre-existing list of potential Genii planets, but that could only take them so far with time this significantly against them.

Add in Doctor Beckett's warnings about the effect that prolonged feedings could have on John, and Elizabeth knew that she had to move quickly. John might have survived for over two decades by himself in an area completely outside his experience, and spent that time fighting some of the most dangerous enemies humanity had ever known, but that didn't mean he could endure that kind of treatment for long… to say nothing of what shape he'd be in once it was all over…

McKay and Ladon had managed to identify a likely-looking planet based on Atlantis's database and the Genii's own files, but when they'd actually checked the address out, they'd found nothing more than a deserted warehouse, with only a couple of caretakers and a few rodents inside. It had been somewhat encouraging to see how quickly McKay and Lorne had rallied the troops to try and save John despite his awkward start in his new role, but Ronon and Teyla were still far too awkward for her to believe that they were comfortable with having John working in the city.

The only thing keeping Ladon alive right now was the fact that she didn't negotiate with terrorists and she was strongly opposed to giving Kolya what he wanted; if that was going to be the last thing John ever said to her, she wasn't going to ignore it.

If only she could stop worrying about what kind of shape John would be in if they took too long to find him…

* * *

As John was forced back into the interrogation chair, he cursed his inability to get through to his fellow prisoner in time to stop this; once he'd started talking about escape, the Wraith had just retreated back into a corner of his cell and sat there in silence.

Still, he supposed that he should be grateful he wasn't going to have to deal with Kolya giving him the apparently-traditional 'villain rant' of pop culture; it might have been different if he'd known that John was the Phantom, but Kolya wasn't going to waste time explaining himself to a Wraithspawn. He'd enjoyed that kind of monologue in the films he'd seen once he was made an official part of life in Atlantis again- one reason he'd liked the _Die Hard_ series was the fact that all four films gave the villain the chance to explain why they were doing this beyond them being jerks- but when you were dealing with that situation in real life and about to be tortured by someone who'd nearly killed the woman he… _CARED STRONGLY ABOUT_… he wasn't that interested in hearing why Kolya wanted Ladon dead.

In end, Kolya's plan came down to the fact that the git didn't have the military strength necessary to mount an effective assault on Atlantis or the Genii right now, so all he had was this twisted attempt at blackmail; the fact that it hurt John was just inconvenient.

As Kolya started to address the camera again, John tried to distract himself by thinking of some of the films he'd seen since returning to Atlantis- the X-Men movies had been interesting, but he had serious doubts about that new _Superman _film that had just come out that year- but when the Wraith walked up beside him and its hand was jammed against his chest once again, John couldn't stop himself from yelling through his gag as he felt another decade or so being taken from him before the Wraith was pulled away.

God… he was going to be reduced to a desk role his first week on the job at this rate…

Aside from vaguely registering that Elizabeth was still rejecting Kolya's offer, John only came back to himself when he was thrown back into his cell. Dragging his way to the wall next to the Wraith's cell, John slumped against the wall and waited for his fellow prisoner to speak.

"You still believe that your friends will come?" the Wraith's strange voice said.

"Yeah, I do," John said, gritting his teeth as he stood up to face the cell window himself. "But that doesn't mean that I want to be stuck here until they pull it off."

"And what would you have us do?" the Wraith asked. "No-one has ever left this place alive."

"First time for everything," John said, looking firmly at the Wraith. "Seriously, though, if you've been stuck down here for this long, what have you got to lose? You know the layout of this place, right?"

"Well enough to know what we would be up against if we attempted to escape-" the Wraith began.

"Which is what I'm counting on," John said firmly. "I'm probably not going to be around for you to snack on for much longer, and they're not exactly going to let you go any time soon; at least this way we can actually do something about that."

The Wraith simply stared at him for a few moments before it sighed.

"You truly believe we can achieve this?" he asked.

"Our odds couldn't exactly get much worse unless you feed on me again," John pointed out. "We bust out now, I'm in decent shape and you're still reasonably fed; if we wait too long, I'm… well, nothing changes for you, but I'm certainly not going to be at my best."

The Wraith simply stared at him for a few moments, before it nodded with a grim smile.

"Like you say, we have a common goal," the creature said at last. "What is your plan?"

* * *

As escape plans went, John could have come up with something more sophisticated, but when his opponents currently believed that he was nothing more than a feral animal, he didn't feel the need to overly complicate things at his end either. The next time the guards came to lead him and his current associate out, John waited until he was outside his cell before he hurled himself backwards, slamming both guards against the bars of his cell and leaving them winded before forcing one to the ground. As the Wraith knocked one of his guard down and started to strangle the second, John punched his own second guard in the throat before turning to the first one as he got back to his feet, slamming the guard's head into the bars of his cell before he could react.

Looking over at the Wraith, John noted with grim satisfaction that the Wraith was feeding on the second guard after managing to get that sheath thing off his hand, but the guard he'd attacked first was back on his feet and firing his pistol at the Wraith's back. Grabbing a knife from the belt of his own fallen foe, John hurled it at the guard, striking him in the back and sending him to the ground. As the Wraith finished feeding, John gave his own foe one last blow to the head to make sure he stayed down before taking the other man's weapon. As the Wraith finished feeding, John tossed his current 'partner' the keys to the shackles on his wrists before taking the guard's radio and other weapons.

With the immediate problem dealt with, John nodded at his new partner to lead the way as the two left the cell-block and progressed along the corridor, heading away from the room where John had been tortured just a short while ago. After a few moments' walking, they were approaching another door with three guards in front of it, prompting John to halt behind a pillar as he took a moment to consider his options. Glancing back at the Wraith- and halting his new ally's examination of the gun he'd taken from another guard- John held up a hand in a 'wait' gesture before activating the radio he'd taken earlier, creating a burst of static from the radios on the guards up ahead. As they looked down, the distraction was just long enough for John to charge forward and stab the man with the knife he'd taken earlier, as his Wraith ally grabbed another guard and broke his neck.

The third guard turned his gun on the Wraith, clearly concluding that it was the superior threat, but John swiftly spun around, using his latest victim as a shield, and fired a couple of quick shots at the other man. The first one just grazed the other man's ear- John's reflexes had been more affected by the feedings than he'd guessed- but the second bullet struck him in the head, putting the guard down and leaving them with a free path to the door. Retrieving his knife, John waited for a moment as the Wraith confirmed that it hadn't sustained any serious wounds before they continued up the base's interior stairs.

After a few moments of frantic ascent, the Wraith opened a metal hatch above them and emerged into the middle of a forest, the world around them dark but the starry sky clear and brilliant above them.

"OK," John said, taking a moment to appreciate the view above them, "we're out; how far to the Stargate?"

"It will be guarded," the Wraith said grimly.

"We've got guns," John noted, indicating the weapons in question; they weren't his usual choice of armament, but when their opponents wouldn't have anything more advanced, he could make it work…

"They will be waiting for us," the Wraith continued, sitting on the edge of the hatch with obvious fatigue.

"You OK?" John said, concerned despite his trained instincts.

"I will be fine… if I feed," the Wraith said, looking at him with a sudden edge to his expression that John didn't like.

"_Don't_," John said, turning the gun on his fellow escapee. "We both know that we need each other right now; we're not going to get out of this if we turn on each other. The Genii are the problem, not us; once we get to the Stargate, we go our separate ways, and that's it. Deal?"

The Wraith simply glared at him for a moment before he got back to his feet, his expression grim but clearly willing to accept John's argument as they began to walk.

"What is the matter with your face?" the Wraith asked curiously.

"My face?" John said, looking at the Wraith in surprise before he tried to fall back on the usual assumption. "I'd think that if anyone would recognise-"

"You are not what they call 'Wraithspawn'," the Wraith said, chuckling slightly as he looked at John. "I would have sensed trace elements of the enzyme in your blood if that was the case; what is there merely suggests brief past exposure to the enzyme, rather than the lifetime that would be expected if you had been contaminated in the womb."

"Ah," John said, contemplating the best response for a moment before deciding to give the Wraith at least some of the truth. "There was an accident… a long time ago."

"Ah," the Wraith said, looking at him in silent contemplation for a moment before he spoke again. "It must have been a… unique accident."

"To say the least," John said, his silence as they continued walking making it clear that he considered the issue closed. Despite the Wraith's injuries, they made reasonable progress, but it didn't take long for John to draw to a halt as he realised something.

"You don't know where we're going, do you?" he said, turning to look at the Wraith in frustration.

"It has been many years since I was brought here…" the Wraith said, even as he sat down on the ground, wheezing as though short of breath.

"Great," John groaned, slumping down on the ground beside his 'partner'. "Our best chance when we get to the damn gate is to take out the guards in a crossfire, and we don't even know where to go…"

"It was not my intention to deceive you, John Sheppard," the Wraith said grimly, as he lay on his back to rest.

John was saved from replying when he heard something coming towards them from the direction they'd been running from.

"Crap," John groaned, as he realised what must have happened. "Not that late… he didn't need much time to deploy guards… _damnit_!"

"Indeed," the Wraith said, looking grimly at him. "There are only four of them, but that is too much for us to confront in this state… unless drastic measures are taken…"

John was about to ask what the Wraith was talking about when he felt the creature's hand slam against his chest once again, followed by the agonising sensation of life being taken from him before he could do more than yell in protest. John tried to protest, but he soon lost the strength to do much more than lie there and groan in agonised exhaustion, feeling as though he'd suddenly become a hundred. He vaguely heard the Wraith roaring as he threw the attacking Genii around, followed by the agonised scream of two guards being fed from, but he could barely focus on anything more than his next breath… it was so hard to focus…

As the Wraith appeared above him, John simply glared up at the creature that had stabbed him in the back in the most dramatic manner imaginable.

"Finish it," he said grimly.

He might be about to die, but he was _not _going to give that Wraith the satisfaction of begging (Even if the bastard wouldn't know who he was really killing)…

"As I told you before, John Sheppard," the Wraith said, "there are many things about Wraith you do not know."

As the hand slammed back onto John's chest, John winced as he felt another biting pain in his chest, felt some part of the Wraith digging into him all over again…

Hold on a minute… he was actually feeling _stronger _now…

As the Wraith took his hand away, John practically shot to his feet, feeling far more alert and prepared than he had any right to feel when he'd been a physical centarian just a few seconds ago. Glancing down at himself, he was amazed to see that his whole body had returned to its original physical age, his muscles back to their peak and his hands strong and firm.

"How the _Hell_…?" he said, looking at the Wraith incredulously. "You can… _give _life?"

"The Gift of Life is reserved only for our most devout worshippers," the Wraith explained solemnly. "And… our brothers."

"Huh," John said, looking down at himself once again before he looked back at the Wraith. "I guess there _are _things we don't know…"

"You have taken steps to give me back my life; I merely repay the debt," the Wraith said.

Stuck for a suitable response to that news, John turned his attention to the easier-to-understand issue of the fallen Genii, soon noting that one was still slowly breathing despite looking as old as he'd felt earlier. "You left one alive, huh?"

"I felt that he would be a useful source of information," the Wraith clarified.

"Good call," John said, nodding in agreement before he walked over to crouch down beside the last living Genii soldier. "OK then, _pal_, we've got a lot to do you already know you're not getting out of this, so do us all a favour and tell us where the Stargate is and how long it'll take; we'll make it quick."

"Straight on… that way… half an hour…" the man said, pointing out weakly with his shaking hand.

"Good," John said, nodding in acknowledgement before he stepped back to let his new partner finish the job; it wasn't exactly pleasant, but John had little sympathy for the people who'd sat back and let him get tortured like that. Picking up their opponents' fallen guns for extra ammunition, John handed a couple of them to the Wraith before they began to hurry in the indicated direction.

After a prolonged period of walking- which was actually shorter than half an hour, based on John's guess; most likely the Genii they'd interrogated wasn't as fit as they were- they had reached the edge of the open area that contained the Stargate. With a lake to the right of the Stargate and six guards gathered around it, it didn't take long to confirm that their options for taking the gate were limited, but both knew that they wouldn't get a better shot.

Exchanging glances with the Wraith, John indicated for him to head to the right while he went to the left. As they moved around the clearing, taking care to hide behind the trees, it didn't take long for John to confirm that none of the soldiers seemed to be that interested in their surroundings; most likely they either hadn't heard about his escape or assumed that he'd take longer to get here.

Once he'd taken up position behind some trees a short distance from the Stargate- he was never going to be able to dial the 'gate before someone saw him, but he was in a safe enough position right now- he quickly studied the trees on the other side, his gaze soon falling on the pale face of his Wraith ally; the Genii wouldn't see it as none of them were looking, but he was in a good position.

Holding up his hand and hoping that the Wraith could see his fingers from this distance, John lowered his fingers one at a time until his fist was closed, at which point he ran from cover and fired at the nearest guard. The weapon wasn't as precise as his usual gun, but the bullet still struck his target in the left side of his chest, knocking the Genii guard down for the count. As John turned to aim at the next guard, taking up position behind the Stargate to use it as a shield, the Wraith dived into action, taking out two guards and charging up to a third, plunging a hand against his target's chest. With John's second target eliminated, before the guard could do more than shoot at the Stargate, John charged out from behind the Stargate and fired at the last guard before he could decide which enemy to go after first.

"Well," John said, shrugging as he looked at the Wraith as it finished feeding. "That went well."

"Quite," the Wraith said, looking grimly at John. "What now?"

"We get out of here," John said, nodding at his ally before he turned towards the DHD, quickly dialling it.

"We agreed-" the Wraith began.

"And I'm not going back on it; I just thought it might be a better idea to get somewhere else before we see about going home," John said, just as he entered the last symbol and activated the Stargate. "After all, do _you _want to stay on this planet any longer than you have to?"

Looking at the active wormhole, the Wraith nodded grimly as he walked up to the gate, John right beside as they stepped through the event horizon to emerge on another world, this one located in a ruined desert city.

"Just a random address I found a while back," John said, as the Wraith looked curiously at him. "There's nobody here and it's fairly off the beaten track; it seemed like a decent choice."

"Agreed," the Wraith said, taking in the area before he looked back at John. "I will depart first."

"Of course," John said, grateful that the Wraith brought it up; he could probably find a Wraith-controlled world easily enough, but by leaving first, he ensured that he wouldn't see John's home address.

"The next time we meet…" the Wraith said, with a new edge to his tone.

"All bets are off," John nodded in understanding.

Still, as the Wraith entered the chevrons for his own address… for the first time in memory, John hoped that he _wouldn't _see that Wraith again.

He wasn't foolish enough to think that he could trust the Wraith completely, but he _could _be reasonably sure that he could trust the guy to stick to any deals they might make if they met again in the future, and he didn't want to have to kill what might be the first Wraith he felt he could trust unless he had to.

As the Wraith walked through the Stargate and the wormhole shut down, John pulled out his stolen Genii radio- from what McKay's analysis had determined, they operated on similar enough frequencies to Atlantis's communications that they should be able to talk to each other if you knew what frequency to use- and quickly entered the address.

The sooner he was back on Atlantis, the sooner he could put Kolya out of his mind until he had the chance to take that bastard out the next time they met…

* * *

Staring anxiously at the Stargate from her office, Elizabeth wasn't sure if the uncertainty was worse than witnessing the actual torture. As long as she could see that John was alive, she had hope that she could get him out, but if she didn't know what kind of state he was in…

She was just relieved that Ladon had agreed to be moved to another room after the deadline for Kolya's last contact had come and gone; he was close enough to the control room that they could still collect him if they needed his input, but until they knew what was up with John, she wasn't going to let her only potential bargaining chip out of the city.

The idea that she could see anyone as a bargaining chip disturbed her on some level, but she pushed it aside; John was important to the expedition, and that was what she had to focus on.

"Has there been any news?" Teyla asked, walking in to look at her, the rest of the Atlantis senior staff gathered in the control room as they anxiously waited for the next call.

"Nothing," Elizabeth said, shaking her head in frustration. "We're far beyond the scheduled check-in time, and Kolya's showing no sign of getting back in touch; we can't keep Ladon contained forever…"

The sound of the Stargate activating prompted her to get to her feet and hurry back to the control room, Teyla close behind her as the wormhole engaged.

"_Hello_?" a voice said from the radio in the control room before Elizabeth could say anything. "_Is anyone there_?"

"_John_?!" Elizabeth said, staring at the radio incredulously. "How-?"

"_I broke out of my cell with the aid of that Wraith that was feeding on me earlier_," John said, sounding almost worryingly healthy for a man who'd been fed on by a Wraith twice. "_I got to the Stargate, grabbed a Genii radio to send this message and dialled out to a neutral planet, but I'd appreciate you letting the shield down so I can come home_."

"Of course," Elizabeth said, turning around to look firmly at McKay. "Let him in."

"But-" McKay began.

"It's John," Elizabeth said resolutely. "Let him in."

With nothing else to say to that statement, McKay reached over to lower the shield.

"It's down," Elizabeth said, hurrying down from the control room as the shield lowered, waiting anxiously for whatever kind of shape John would be in when he returned; if he could make an escape, he couldn't be _that _badly off, but-

When he walked through the Stargate, looking no older than he had the last time he'd set foot in the city, Elizabeth was relieved that she wasn't the only person to gasp in shock; even with John's hands covering the more damaged parts of his face to avoid shocking anyone, it was clear that he showed no sign of the physical aging he'd been subjected to.

"What the _Hell_?" McKay said, looking at him incredulously from the control room. "How- you were- I mean, you look younger than you did before you left!"

"Turns out Wraith don't just take life; they can also give it," John explained with a slight chuckle that was only partially muffled by his hand. "We had to take out a few guards on the way to the Stargate, and my old cellmate took the opportunity to feed on some of them and give me back the years I'd lost."

"Seriously?" Lorne said, looking at the disfigured man in surprise. "He just… _did _that?"

"He referred to it as him 'repaying the debt' of me giving him back his life," John said. "Of course, I'd have preferred it if he'd consulted me before using me as a battery pack for the last round- he needed my energy to give him the strength to fight off this guard team we ran into- but when the alternative was to be dead or recaptured, I'll take what I can get…"

Elizabeth didn't care about the finer details right now; all that mattered was that John was back, he was away from Kolya, he was safe in Atlantis, safe with _her_-

She froze, overwhelmed by the intensity of the feelings she'd only just acknowledged.

The idea of losing John Sheppard had scared her.

The revelation that she loved him was terrifying.

If she hadn't been in public, Elizabeth would have screamed in frustration and then broken down sobbing.

She'd known that she had an attraction to John for some time- her 'hallucination' while under the influence of Oberoth's nanites had proved that- but the idea that she _loved _him…

Even if he was technically outside of the standard command structure, he could never see her that way; she represented the peace he'd been striving for since he'd come to Pegasus, the representation of the promise he'd made to his only real mentor and guide…

God, he'd met her when she looked like she was in her eighties; even if that hadn't technically been _her_, it was still weird.

Resolving not to think about it any more, Elizabeth made a brief comment welcoming John back before she turned around and headed back for her office, making brief comments about needing to start arrangements to send Ladon back to his people with her full apologies for recent events; hopefully the Genii would all understand that she'd just been anxious about the absence of an important member of her staff…

_Shit_.

John was just settling into his new role on Atlantis, and now she had to make it all complicated by realising that she was in _love _with him?

She hadn't been expecting this…


	6. The Digital Ark

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: Another shorter rewrite, but that's the way things go; I skimmed over a couple of details, but I hope you'll like the result anyway.

Clash of the Phantoms

Having finally reached a point where he could take his spacesuit off after spending almost an hour walking around inside it, John revelled in the restored ability to scratch around his facial make-up; it was still taking a while for him to get used to this arrangement, but he really appreciated the results.

He knew that he could never regain his old appearance- and in some ways, he didn't want to; the fact of the Phantom was a face that represented the war he'd survived for so long- but even if putting on the make-up took up a lot of time, it was nice to feel normal again, after so long standing out from the crowd at a glance due to his mask or his face.

Besides, after spending the better part of the last week being tested and debriefed following his brief captivity, as well as undergoing all kinds of tests to confirm that there had been no side-effects from his treatment by the Wraith, it was good to be getting back to his new usual routine. Once he'd been checked out and cleared of any potential medical side-effects, the IOA had tried to use John's capture against him, arguing that it hardly boded well for Atlantis's military structure if their military commander could be abducted that easily, but John had neatly countered their arguments by pointing out that he could hardly be held responsible for being taken by surprise on what was meant to be a diplomatic mission to a peaceful planet. Since nobody could legitimately claim that John should have been prepared for anything without giving the impression that they wanted a brutal soldier rather than a more rounded individual, the IOA had been left with no real other choice than to allow the former Phantom to continue as the expedition's military leader.

Still, the team's current mission had seemed to be a relatively simple one when they'd received the original assignment; they'd found an unusual space station located near the space gate that was the next address listed in the database, with no trace of life signs and relatively minimal power readings. After taking a puddle jumper to the small asteroid-esque moon where the base was located, with a docking bay containing two other antiquated shuttles, John and McKay had donned a couple of spacesuits and set out to explore the base, which had a technology level that McKay compared to Earth in the 1960s if the space program had managed to make greater progress.

John had been uncertain about its potential value, but he had agreed with McKay's decision to explore it in greater depth before giving up the search, resulting in them searching through the various corridors until they finally found a hatch leading to the complex's control room. Once McKay found the controls for the base's power supply, he had turned them back on before John could stop him, the Canadian scientist eagerly anticipating the possibilities of exploring the base and the attached shuttle until he'd detected an apparently familiar energy signature from another part of the complex. John had taken a moment to alert Teyla and Ronon to the possibility of a problem as they remained back in the puddle jumper before hurrying after his associate.

After finding a map of the complex on the facility's computer, they'd managed to track the source of the energy signal, quickly making their way to the location in question. Once they had arrived at the appropriate room, they'd discovered a large device covered with glowing green panels in a large metal cradle, with a second empty cradle beside it, and a man lying on the ground wearing what looked like some sort of boiler suit.

Whatever this place was, there was clearly some kind of mystery here that meant they weren't going to leave here any time soon.

As he removed the last of his suit to make exploration easier, John mused that he might be calling Atlantis a bit earlier than he'd anticipated, but at least this time he'd be giving Elizabeth relatively positive news, as opposed to the dire nature of their last mission…

* * *

Ever since John had come back to Atlantis after his period as Kolya's prisoner, Elizabeth had dreaded the moment that she would have to send him out into danger.

It was irrational to be terrified for the safety of a man who'd survived by himself for over two decades when he was being hunted by virtually an entire galaxy, but she couldn't help it; it was just…

_God_.

Every time she tried not to think about it, she just kept coming back to the original problem; even if John respected her as a leader and friend, she obviously wasn't his type.

She'd never dared to confess it to anyone, of course- even with doctor/patient confidentiality, something like this just felt too personal to admit even to Doctor Heightmeyer- and she wasn't even entirely sure how she felt about this herself…

All she knew was that, during those brief few hours when she hadn't known what had happened to him as he remained in Kolya's custody, Elizabeth had never been more terrified… and even after she'd acknowledged why she was so scared, she couldn't afford to share it with anyone. For all of John's reassurances to her that she meant a great deal to him, not only was she far from a suitable partner for a man who regularly risked his life for the galaxy against a race of vampiric aliens, but he'd met her- even if it wasn't _her_, from a certain point of view- when she was an old woman in her physical eighties; how could he ever see her as someone to be… _intimate _with?

She respected him as a colleague and valued him as a friend, but she was starting to want so much more from him than he could ever be expected to share with her…

Right now, however, she had more immediate concerns in the form of the unusual moon complex that John's team had just discovered. The technology as a whole might be primitive, but she had to admire the spirit that had driven a planet's population to attempt something like that, even if their exact motives were still a mystery, to say nothing of their latest discovery.

"You reported that there were no life signs," she said, as John revealed that they'd discovered someone in the lunar base. "How did he get there?"

"_We don't know yet_," John replied grimly over the radio. "_There was some kind of energy spike right when his life signs popped up, but we're still working on what that meant_…"

"_Actually, I just solved that_," McKay's voice interjected. "_I recognised the initial energy signature as very similar- virtually identical- to Wraith beaming technology, so I ran a further search, and it looks like he was automatically reintegrated when life support systems started up_."

"Beaming technology?" Elizabeth repeated. "A minute ago you said the station was antiquated?"

"_Other than that particular upgrade, anyway_," John explained.

"_And the artificial gravity_," McKay added.

"_That's artificial gravity_?" John asked. "_I thought it was just a very dense moon_-"

"Getting back to the beaming technology?" Elizabeth asked.

"_Well_," McKay continued, "_I'd need to take a closer look but I am pretty sure that that device is modified Wraith technology, probably from a crashed Dart. If you think about it, it's actually a brilliant fusion of_-"

"And what do you intend to do with this person we've now assumed responsibility for?" Elizabeth interjected.

"_Oh… I dunno_," McKay noted. "_I didn't think that far ahead_."

"Obviously not," Elizabeth said (She was aware that she was possibly venting her frustration about the situation with John against McKay, but she was in no mood to try and calm down when she had something to vent about). "You need to keep in mind that if one person beamed out of nowhere-"

"_There may be others where he came from_," John finished for her. "_I was thinking the same thing_."

She heard Teyla say something off to the side, but was saved from asking what had just happened when John spoke again. "_Alright, we'll find out in a minute. Our boy's waking up. Call you in one hour_."

"One hour it is," Elizabeth said, before John terminated the radio link, leaving her to smile hopefully at this news.

If what she'd heard was accurate, she hoped that the best-case scenario for the situation described would turn out to be correct; after John's last bit of difficulty offworld, it could do him some good if he managed to save someone once again.

* * *

Listening to the story told by their new associate- who'd introduced himself as Herick- John wasn't sure if he should admire this planet's former population or pity their desperation.

As far as methods of escaping the Wraith went, deliberately destroying your entire planet in the hope that you could rebuild after it had recovered was a very extreme way of doing things, but it had the luxury of being something that nobody would have thought of before. While Herick's explanation that he'd been expecting defeat at least explained why he hadn't shown much of a reaction to McKay's talk about what had happened to his planet, the revelation that there were others in storage had been more of a surprise, particularly when even McKay was apparently impressed at their ability to use Wraith beaming technology as a storage system.

John wasn't sure that he'd go as far as these people had done to save their lives by destroying their planet, but he had to admire the goal and determination even if he doubted their methods. Unfortunately, Herick had been shocked to learn that there was only one shuttle stored in the facility rather than the two he'd been expecting to find, leaving him and Ronon to follow their new associate to the pattern storage room when he tried to reactivate the system.

"They were to launch within hours of us," Herick said, as he frantically tapped away at a panel on the device. "Jamus gave me his word."

"Maybe the Wraith got to 'em before they could get to it," Ronon noted

"No," Herick said firmly as he tapped away at a set of controls. "They were ready; I spoke to the pilot myself. They were just hours behind us."

"What are you doing?" John asked the other man, as McKay called to report another power-spike.

"Getting answers," Herick said, before he pressed a button, causing the device to generate a beam similar to a Wraith transporter beam that deposited an older man in the room, wearing a blue version of Herick's suit. John and Ronon quickly pulled out their weapons, but they didn't even have the time to do anything before Herick charged forward to grab the other man, yelling something about how 'they' should have been there he awoke before John pulled them apart.

"All right," he said, glaring at the two men, trying to channel the authority he normally saved for his appearances as the Phantom. "Let's take it easy and give this guy a chance to breath, OK?"

"I… I don't understand…" the new arrival said, looking between the three men in confusion.

"Where is the second storage device?" Herick said, indicating the empty cradle beside the original device. "You _assured _me that my family would be on the second storage device, Jamus; where _is _it?"

"They waited too long to launch the second shuttle," the old man who was apparently Jamus replied. "Herick, I'm sorry."

"I worked every day of my life to complete this place with the promise that when it was done, my wife and son would be among the ones saved," Herick said, glaring at the old man. "You made me that promise, when you stored my pattern in the device."

"Shortly after you were stored in the device, word came from the planet that the last group had not yet made it to the second shuttle," the other man explained with genuine regret. "With the launch of the first just hours before, the secret was out. There were riots on the street. Much of our leadership was in that last group."

"You delayed the launch," Herick said, as Jamus got up to pace. "How long did you wait?"

"A day, but in that day the Wraith came, Herick, through the Portal," Jamus explained. "We knew it was the beginning; we knew it was an advance scout. It had happened far too many times in our history. We knew."

"Why didn't you order them to launch?" Herick asked, as he leaned over the device.

"Because the second shuttle would have led the Wraith straight here," Jamus said, firmly only able to stare apologetically at the other man's obvious grief and horror. "It was the only way; you _must _understand that."

"Sounds to me like you did it to save yourself," Ronon put in grimly.

"No; to preserve those already in stasis," Jamus said, indicating the storage box beside Herick, before walking up to focus his attention on his colleague. "If the Wraith had followed the second shuttle, if they'd discovered what we had done, they would have blasted this moon from the sky. It was the hardest decision I have ever made, but if I had not made it, your life's work would have meant nothing."

"Another life sign just appeared on the shuttle's H.U.D.," McKay called out as he walked into the room, smiling as he noticed the new arrival before he offered him a handshake. "Oh, hi, Doctor Rodney McKay; I was the one who powered up your station."

"My people are… grateful for your assistance," Jamus said, after McKay lowered his hand once he realised that he didn't know what the other man wanted to do about it.

"We don't need them," Herick said.

"We _do _have a ship," John noted, his suspicions about the other man growing with that comment; considering that the guy was only even out of storage because they'd arrived, he thought that made it clear that these people _did _need them.

"One that- no offence- is better than that shuttle you've got there," McKay added with a satisfied smile. "We can get you back down to the planet and restoring your civilisation in no time."

"Does your ship have an internal power supply attuned to the storage device?" Herick asked, prompting the Canadian scientist's smile to falter.

"Herick wishes to finish the task that will complete his life's work," Jamus put in, walking up to Herick. "And when you have flown our people back to the surface, then the new era we have dreamed of will begin, free of the Wraith for all time."

"For all time," Herick said solemnly, as the other man gave him a reassuring pat on the shoulder. "Forgive me; I must prepare the shuttle for launch."

"Of course," the other man said.

"Look, if you want a hand with the control room, I could, um…" McKay began, only to be ignored by Jamus as Herick walked away without looking back.

"We'll… leave you all to it," John said, nodding briefly at the other man as he left the storage back with McKay and Ronon, turning to address them both once they were in the outer corridor. "OK, McKay, see what you do about making sure that shuttle's in working condition; I'm going to keep an eye on Herick."

"You think he's going to kill that guy?" Ronon asked, indicated the room they'd just left.

"Either that, or he'll kill himself," John answered grimly. "And given the limited options for doing that up here, I'd like to make sure he doesn't do anything stupid…"

After quickly confirming to Jamus that they were sticking around until everyone was back on their planet, John walked briskly after Herick, finally finding the man as he was confronting Teyla in a corridor at the end of a series of open pressure hatches.

"…not caused by the Wraith?" Herick said, glaring at the Athosian woman in exasperation.

"Still, if there is anything we can-" Teyla began.

"You've done enough," Herick said grimly.

"I do not understand," Teyla said uncertainly.

"If you had never come, if I had never awoken, my last thoughts would have been of hope for the future, and the love I have for my family," Herick said coldly. "I never would have to feel what I feel now. Gather your team and leave this place."

"We'll get to that later," John said, stepping out from his corner to look resolutely at the other man. "Right now, I'm just going to make sure _you _don't do anything stupid."

"I have lost _everything_-" Herick began as he turned to glare at John.

"And I lost almost the same thing, which is almost worse because there are several reasons why I _can't_ get it back even though my old life's still there; you've at least got a chance to rebuild a new life without dealing with old ghosts," John said grimly. "I can appreciate that you're grieving right now, but I have seen a _lot _of people in your position make serious mistakes, and I'm not going to trust you to leave my _sight _until your people are safe."

"You have no right to judge-!" Herick began, before John sighed and slammed his fist into Jamus's face, striking him with such force that the other man was sent flying for a few feet before he fell to the ground in a heap.

"Was that necessary?" Teyla asked, looking at him in a critical manner.

"Believe me, when you've seen as many Wraith-devastated worlds as I have, you learn to recognise when you're dealing with the kind of guy who just wants the pain to end even if he'll end up taking everyone else with him," John noted grimly, glancing down at the unconscious man on the floor before he looked back at the Athosian woman. "Help me get him somewhere secure and then we can see about dealing with all this."

Despite the still-present tension between them both, John was grateful when Teyla went along with his request. Their working relationship was still tainted by her knowledge of his true face, but she was at least willing to work with him with relative ease, where Ronon always seemed to be looking for a reason not to trust him.

* * *

Once Herick was confined in a cupboard area until they could get him on a more effective 'suicide watch', John had called in another team from Atlantis to assist them in getting Jamus and the rest of his people back down to the planet. A quick scan with the puddle jumper had confirmed that the planet's ecology had already started to recover following the devastating bombardment that had originally rendered it uninhabitable, and the now-activated shuttle had sufficient fuel for a return flight, so all that they really needed to do was find a suitable landing-site and make their plans accordingly.

The storage device had been confirmed to be fully functional and ready for them to activate, but John agreed with Jamus that it would be best to do it once the shuttle had been brought back to the surface, as they couldn't control who'd be released from the device in any particular order and didn't want to risk having to deal with any children or anyone else who wouldn't be much help in the current situation. Herick had been apparently assigned to be the pilot for at least one shuttle for the return to the planet, but considering the man's mental state, John had volunteered to pilot it himself while Herick was put back into the storage device and the rest of John's team returned to the puddle jumper.

It had taken a few moments to adjust to a ship that _didn't _just obey his every command, but thanks to the training he'd received in piloting the F-302s, it was relatively simple to get a handle on the relevant controls for the shuttle. Once the jumper had launched from the lunar base, John had disconnected the shuttle's docking clamps and taken the ship back towards the planet, aiming for the location that Jamus and McKay had earlier identified as the most lively-looking area on the surface. The actual landing had been a bit close when the ship's landing-gear didn't work at first, but it landed in a reasonably intact condition, leaving the Atlantis team free to activate the storage device and release its 'passengers' back onto their world.

The flight itself might have been a bit bumpy, but once they got down, everything had gone fairly smoothly as far as John could see; everyone seemed to be fairly enthusiastic about the chance to rebuild their world, they were all grateful to be reunited with their families, and he'd even seen Herick smile slightly as he took in his 'rejuvenated' world once they'd reached the surface.

"Funny, isn't it?" McKay mused, as the team stood by the puddle jumper to watch Jamus brief the first wave of survivors from the storage device on what had taken place.

"What is?" John asked.

"How simpler things are with you in charge," McKay clarified. "I mean, if Colonel Sumner had been here… well, to be blunt, we'd probably have missed Herick's mental state, he could have done something drastic like open the airlock, and then we'd have had some actual _trouble _with this situation instead of a smooth ride…"

"Things just worked out," John shrugged, wondering what they were going to do with Herick in the long term before dismissing that as someone else's problem; he seemed to be past the worst of his initial grief, and Atlantis couldn't exactly afford to become the psychiatric hospital for all of Pegasus. "Like I told Teyla, I've been around long enough to know how people react when they've lost families to the Wraith; you learn to anticipate who's going to take it badly."

"There have been times where you failed?" Teyla said, looking at him in surprise. "We have always heard tales of the Phantom's successes-"

"Because there generally aren't any survivors left to talk about the occasions when I blew it," John noted, his expression grim as he looked at the Athosian woman. "I didn't become a legend overnight, Teyla; even after I started wearing the mask, it took a while before I got things right."

The tension in John's shoulders was enough to discourage even Ronon from asking for further information, despite his curiosity at this hint John had just provided about his past.

"Well," McKay said, shrugging as he looked at the rest of his team, "we gave a civilisation a chance to start again; not a bad day, right?"

* * *

Lying on his bed after returning to Atlantis, the man once known solely as the Phantom stared uncertainly around his room.

Of all the changes he'd experienced since returning to Atlantis from Earth, having his own quarters was simultaneously strange and a refreshing return to normality. He might have spent almost three years hiding around the city's air ducts to escape being caught by the expedition's security forces, but he'd spent longer than that living in Atlantis on his own.

The only strange bit was having specific quarters assigned to him; since he'd spent so much time exploring the city on his own when he'd arrived, he'd developed a tendency to just crash in the first room he found when he got tired, and now he had his own specific place?

He'd kept the various possessions he'd picked up from his old room in case he felt the urge to decorate later, but as it was he just didn't feel a real drive to do much; he had the box they'd been transported in waiting in a corner for when he was ready, he had a wardrobe for his clothes, he had a few books he was browsing through to catch up on what he'd missed out during his time away from Earth…

A knock on his door cut his thoughts short, but when he let out a brief acknowledgement, he soon sat up when the person on the other side walked in with her usual warm smile.

"Hi," Elizabeth said, studying the surroundings with a slightly sad smile. "Still working on decorating, I see?"

"I got used to moving around a lot when I slept here on my own," John clarified as he looked back at her; he appreciated her concern, but he felt obligated to assure her that all was well. "Giving myself time to get comfortable before I do anything like that; you know how it is."

"Of course," Elizabeth smiled at him in understanding before she looked more curiously at him. "I read your report about your last mission, and… well, you didn't approve of what they did, do you?"

If anyone else had asked him that question, John wouldn't have answered it, but when he had spent so long keeping so many secrets from Elizabeth- and was still keeping at least one from her- he tried to make up for it being honest now.

"No," he said, looking grimly at her. "I get _why _they did it, but I don't agree with the method; they may have picked their best and brightest to survive for the future, but they still basically allowed their entire civilisation to blow themselves up so that the Wraith wouldn't realise some of them got out before the bombs fell."

"Jamus said that they used their nuclear bombs on the Wraith ships-"

"And he also stated that only a small percentage of the population knew about the evacuation plan," John interjected. "I can admire the whole 'needs of the many outweigh the needs of the few' philosophy, but not only is this the other way around, but the many didn't even have a choice in the matter. Desperation can only excuse so many atrocities before it won't cut it any more; I've made choices to save some people and leave others behind, but that's not the same as making the decision to kill most of your population so that some of them can survive."

Elizabeth said nothing as she walked over to sit beside John on his bed, before reaching up to place a reassuring hand on his shoulder.

"For what it's worth," she said, smiling slightly at him, "I agree with you that what they did was terrible, but… well, considering everything they accomplished with relatively limited resources, they could be useful allies in future, and we can't judge all of them for the decisions that their leaders made in the past."

"Hey, believe me, I've no intention of tarring the whole population with the same brush; I'm just saying why I don't agree with what they did to their planet," John explained.

"Good," Elizabeth said. "Major Lorne's dropping off some additional supplies; I thought it best that you get some rest after all that."

"Thanks," John said, nodding gratefully at her.

Whatever else had happened on that planet, McKay was right about one thing; their actions _had _saved an entire civilisation.

John just wished they'd been able to save the people from themselves…


	7. The New Hero of Pegasus

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

"_Another _hero in this galaxy?" McKay said, looking sceptically at Teyla as the team prepared for their next mission. "I thought the Dark Knight here was it?"

"I'm not Batman, McKay; I'm the _Phantom_, remember?" John pointed out. "If nothing else, it's a more generic name that limits the risk of me being sued for copyright infringement…"

"Batman?" Ronon asked.

"Fictional character back on Earth; he lost his parents as a child and dedicated his life to make his city a place where that couldn't happen again by training for years and then adopting a costume that made him look like a giant bat so that he could scare the criminals he was hunting," John explained.

"Getting back to the current topic, why aren't you going all-out?" the scientist added, looking curiously at John, who was only wearing the standard Atlantis uniform and his simpler facial make-up. "I mean, if we're meeting the first addition to the Pegasus Avengers-"

"_If _I decide to form a team of any sort, I'd prefer to form an impression of this guy when he's _not _trying to impress 'the Phantom'," John clarified firmly. "In case you haven't noticed, the mask tends to result in people reacting to me in various extremes; there's never a middle ground."

He paused for a moment to give the others the chance to remember their own reactions before he looked back at Teyla. "Anyway, what _do _we know about this guy?"

"Very little," Teyla noted. "The Athosian who spoke to me of his deeds simply referred to him as a great hero of the town, a warrior who possesses almost superhuman-like powers."

"For what it's worth, we do know that this planet has a good reputation in terms of its status as a trading location; I just don't recall hearing about there being any superheroes in that area," Elizabeth put in.

"They're helped by the fact that they're a bit outside the Wraith's usual hunting territory," John noted, before he shrugged and indicated the Stargate before them. "Anyway, time to go and see if this guy lives up to the rumours, right?"

"My fellow Athosian confirms that he saw this hero in action against several armed men," Teyla noted as the Stargate activated, the warrior woman looking at John in a particularly critical manner.

"Not doubting anyone's word; just wanting to be prepared for anything," John clarified, as the Stargate made its connection. "Anyway, let's go."

* * *

Walking through the village where their mysterious 'hero' was apparently located, John allowed himself a few moments of idle speculation as he wondered how a world like this could have produced the hero they were apparently here to meet. It wasn't that the place didn't seem like a pleasant enough environment- even if the clothes reminded him of the Genii's usual 'disguise' before they revealed their true natures to anyone- but it just didn't seem like the kind of place that _could _create someone like the stories they'd heard about…

Still, after the rest of his team had spent so much time talking about their own personal heroes, ranging from McKay's admiration of Batman to Ronon's admiration of his original unit commander, John was relieved when one of the villagers came up to talk to them before anyone tried to ask him for details; he wasn't sure how he could answer that question honestly without revealing a couple of secrets he wasn't willing to share…

"Good day, travellers," one of the villagers said, smiling warmly at them after they had walked through some rather appealing gardens around the buildings.

"Good day to you," Teyla replied.

"This is your first visit to our village?"

"Several of my people have said that you are good and fair traders," Teyla said.

"We are," the man replied with a warm smile.

"My fellow Athosians also speak of a great hero who protects this town."

"Rumour has it he's a warrior with some impressive kills to his credit, including the Wraith," Ronon added.

"That is true," the man smiled.

"Then, uh, there's a good chance he's one of _my _people," Ronon added with a grin, prompting John to look at him in frustration.

"Can you take us to him?" Teyla asked, deciding to avoid that particular question.

"Of course; this way," the man said, indicating another small street. As the team followed him to the town square, John wondered what they were about to find, but when he heard the sound of someone laughing in a familiar manner, he started to harbour his doubts about this 'hero'…

"Here he is," the man said. "Our champion protector, Lucius Lavin."

The second he saw that overweight prick sitting on the edge of the table in one corner of the square, John had to remind himself that attacking the man, while satisfying to him, wouldn't do anything to endear them to the local villagers.

"Well!" Lucius said as he grinned at the four of them before his gaze focused on John. "Would you look who it is… and you are?"

"You've got to be kidding me!" Ronon said in exasperation.

"Colonel John Sheppard," John said, as Lucius looked inquiringly at him; his title might be a provisional rank at best, but he'd been given special dispensation to use it when dealing with alien worlds.

He might have to tolerate this git's presence if he was going to learn what was really going on here, but he was going to need to _really _concentrate to make sure that he didn't give into temptation and stab this bastard on principle…

* * *

Listening to Lucius telling his stories to the enthralled townspeople, John wondered how this bastard managed to get people to be so interested in his mountain of crap. His current story about escaping a burning building with various women and children while fending off an Iratus bug attack in the process was so outrageous it reminded John of a bad action movie, but it was mainly an opportunity to keep the man occupied while Doctor Beckett took a quick blood sample to test.

Quite frankly, John wished that they could have just resorted to the simpler option of knocking the berk out; the man's ego had apparently quickly recovered from the humiliation of the Phantom trapping him in Atlantis's cell during their last meeting, and he was as chipper as ever. Even when John pointed out a hole in his story of leading people out through a blocked entrance, Lucius simply backtracked and claimed that he had 'bravely' cleared a path through the fire while passing over how he achieved it.

If it wasn't for the fact that it wouldn't get him anything but a moment's satisfaction, John would have revealed his identity as the Phantom just to make the prick shut up…

"So," John said, as Lucius waved the villagers away with talk about the story of how he was 'almost seduced by an Ancient', "you have some very… familiar stories…"

"I admit, I took some… inspiration from some of the mission reports I perused while I was on Atlantis," Lucius said, shrugging awkwardly before he looked more curiously at John. "And I never met you while I was there…"

"Colonel Sumner decided to return to Earth a couple of months ago; I was… appointed as his replacement," John said briefly; he wasn't about to tell this man anything about his past as the Phantom even if their last encounter hadn't been particularly tense. "That said, I _did _read the reports about what they've dealt with before I joined them, including the one about that herb you used last time…"

"Oh, you're not gonna find any of _that_ in my system," Lucius said with a reassuring grin. "I learned my lesson about that while I was on your city."

"So these people simply… adore you for who you are?" Teyla asked cynically.

"Exactly!" Lucius grinned. "Ain't it great?"

"I doubt it," John said, glaring sceptically at the former baker. "Your reputation doesn't exactly do you credit…"

"You worry too much," Lucius smiled. "In all modesty, these people love me, pure and true."

"Lucius, after everything I've read about you, I'd want to double-check if you told me that rain was wet," John informed the baker bluntly.

"I _saved _them!" Lucius protested. "I drove away this bunch of ruffians a couple of months ago, and ever since, I've been the town hero; they give me gifts, the women are throwing themselves at me… it's like the old days, except better, because _now _they're not drugged."

"Hang on, hang on; _you _beat them up?" McKay interjected sceptically.

"Yes!" Lucius said firmly. "Me! I did!"

"How'd you manage that?" Ronon asked.

"It's not so hard… when you're invincible," Lucius grinned.

"Really," John said, slipping one hand under his flak jacket as a possible explanation came to him. "Let me test that…"

Before anyone could ask what he was doing, John reached over and slapped Lucius on the back of the head, grinning as Lucius yelped in pain before looking at him in shock.

"What?" Lucius asked, staring at him in shock. "How- I've-"

"You're using one of these, right?" John said, opening his jacket just enough to reveal the Ancient shield device he always carried with him when he was going off-world; he might not wear it full-time to ensure that he could keep it charged up for when it really mattered, but whether he was acting as John Sheppard or the Phantom, something like this could always be useful. "Unfortunately for you, so am I, and as anyone with any _sense _or _experience _knows, when two of these shields come into close proximity, so long as they're still on factory settings, they basically recognise the other shield as 'self' and allow it to pass through their barrier."

"Huh," Ronon said, looking at Lucius with a thoughtful smile. "Well, at least that explains the 'hero' bit."

"How did you even turn that thing on?" McKay asked sceptically. "The last time I checked, you didn't have the Ancient gene, and Jo- the Phantom left you stuck in that cell before we could give you the gene therapy…"

"Well, I found it as one of various gifts I'd received in the past, and was able to find someone else with the gene to get _them_ to turn it on for me…" Lucius explained, shrugging with a casual smile. "What can I say? I perused a lot of mission reports while I was visiting."

"Right," John said, looking sceptically at Lucius for a moment before he sighed and turned around, leaving the rest of his team to hurry after him as promptly as they could despite the unexpectedness of the decision.

"Are you sure this is-?" Teyla began.

"The man's clearly just playing on the tech rather than the drug to get people to like him this time around; we've got bigger things to worry about than some moron who thinks he's got a good scam going," John said firmly, taking a brief glance around to make sure that they were alone before he continued speaking. "Besides, after what that git did to you all last time we saw him, if I didn't leave now, I'd rip his balls off and make him eat them."

"Ah," McKay said, his face paling slightly as he looked at John. "Thank you for that… vivid mental image."

"You would do that to him for being annoying?" Teyla asked critically.

"I would do that to him for turning… some of the strongest people I know into pathetic sycophants hanging on his every word because he couldn't accept that he was just a pathetic git," John clarified, only just remembering to control his response; he might have an official position now, but that just made his position more precarious in some ways, particularly when it came to Elizabeth. "The fact that he's annoying while he's doing it just makes it easier; the man has nothing more to offer than his ability to be a git."

"And the fact that he has an Ancient shield device-" McKay began.

"Means nothing because I doubt he's kept everything he got as a gift on the last world if he's had to leave his old one, he's almost certainly used up most of its power by now if at least half the stories we've heard are anything to go by, and if you really want to study one I've got a couple in storage that I'd be willing to let you have a look at if you asked," John said, shaking his head as he glanced over at McKay. "Like I said, let's just get out of here before he pushes me further."

"Quite…" Teyla said, looking at John with a slightly apprehensive glance before she shrugged uncertainly. "At least we can confirm that he is not brainwashing anyone this time."

John decided to leave that whole topic alone; Lucius might not be actually using mind-altering substances now, but lying to people wasn't that much of an improvement, however he looked at it…

They were only a comparatively short distance from the town when the sound of yells and gunfire were heard from the village; even at this distance, the sound of weapons being fired was fairly distinctive. Taking a quick glance at his team, John had soon turned around and was leading them back to the village, weapons drawn in case of any trouble. A few additional gunshots were heard as they hurried towards the town, but when John noticed some people running away from the town, dressed as though they were stereotypical bad guys in an old Western, he quickly changed his mind.

"OK," he said, holding out a hand to halt his team as he indicated the departing men. "McKay, Teyla, get into the village and see what you can find out regarding what just happened; Dex, follow me and see if we can find out where those guys are going."

Nodding in agreement at the division of labour, the team quickly split into their assigned responsibilities, Teyla and McKay heading into the village while the two soldiers turned their attention to the escaping men.

John didn't know what was going on here, but something about those guys rang a bell…


	8. The Phantom, the 'Hero', and Kolya

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

It didn't take long for John and Ronon to get a good feel for what they were dealing with. The men they were following were clearly trying to take a rather complex route to their destination to escape anyone who might try and follow them, but it was equally obvious that their plans were based around the assumption that someone would try and follow them from the village, rather than spot them leaving it from the outside. With Ronon and John able to keep track of them from two different angles, combined with their shared experience at tracking far more dangerous prey, it didn't take long for them to find what had to be the mens' camp, a short distance from the Stargate and the village, set up in a manner that made it clear it was only a temporary establishment rather than any kind of long-term dwelling.

As far as John could tell from a cursory examination, none of the men appeared to be particularly injured, which left him with the question of what had just taken place; in his experience, men armed with automatic weapons attacking a village like that one didn't just run off without taking some fire beforehand…

"What are we doing here?" Ronon asked, after they had been sitting in position for almost half an hour just watching the soldiers mingling around the camp.

"Waiting for my theory to be confirmed," John said.

"Your 'theory'?" Ronon repeated, looking at John sceptically.

"Ronon, do you honestly think that anyone serious about attacking that village would back off that quickly just because some fat guy hit back at them?" John noted. "We both saw that those guys were armed, so they should have tried to wear the shield down or something like that rather than just scuffle for a few minutes and then leave; this whole situation smells, and I think we can both guess who dealt it."

Ronon looked at him in silent thought for a moment before he nodded in agreement and resumed his original position. With each man's mutual experience at staying hidden, coupled with the advantage that nobody in the camp was actually expecting someone to have followed them, it was easy for John and Ronon to keep watch until Lucius finally walked into the camp, his casual conversation with the men making it clear that John's theory had been correct.

In a grim manner, John was glad to have evidence that he'd been correct about Lucius; the guy might have moved on from drugging people into liking him, but setting up fake threats was far from an improvement. They were slightly too far to hear what Lucius and the mercs were talking about, but from what John could see and hear, it appeared that the men he'd hired were angered at the extent of injuries Lucius had inflicted on them during their mock fight. John thought that things would calm down when Lucius tossed them a bag of money, but judging by the expression on the man's face when he looked at the bag's contents, he evidently wasn't satisfied with the amount that Lucius had chosen to pay him with.

"Trouble?" Ronon muttered, glancing over at John as the lead mercenary argued with Lucius.

"Most likely," John confirmed grimly, eyes fixed on the confrontation taking place before them. "Lucius really needs to realise that the shield doesn't stop him being _injured _by any determined enemies before he does something stupid…"

"Should we try and make them talk?" Ronon asked.

"No offence intended to those people in the village, but even if they believe we didn't force a confession, are they really likely to believe us over the guy they think has been saving their asses recently?" John pointed out. "I mean, Lucius doesn't strike me as smart or brave enough to come up with this kind of scam from nothing, so he probably _did _save the village from the first wave of mercenaries, and we don't really have anything that would make these people believe us over him…"

"Except the word of the Phantom," Ronon noted with a pointed stare.

"Which is something I'd rather not resort to for something this… petty," John said, looking awkwardly at Ronon. "The Phantom's meant to be a selfless protector against the Wraith; as much as I think Lucius is a git, I'm not going to compromise that persona just to teach him a lesson."

"So what _do _we do?" Ronon asked, after looking thoughtfully at John for a moment before nodding in acceptance.

"Judging by the way these guys are looking at him," John said, indicating the small camp glaring after Lucius as he walked back to the village, "I'm thinking that we stick around for a little while until someone decides to do something stupid, then step in and make the fat git see sense once they tip their hand but before things get ugly."

"Sounds like a plan," Ronon agreed.

* * *

After returning to the village, John had to wonder if dealing with the villagers' hostility for trying to 'expose' Lucius wouldn't have been worth the risk. When he got down to it, his speculation about what the mercenaries might do if provoked was really nothing more than guesswork, and if these people were stupid enough to believe everything Lucius had to say to them, they almost _deserved _to get shot…

He knew that he wasn't going to do anything like that, but he was allowed to 'fantasise' about what he might do to this prick after everything he'd done during his last visit to Atlantis. McKay and Teyla hadn't been entirely happy about the plan either, but Teyla was at least willing to acknowledge that the village had to be protected regardless of their feelings towards Lucius, even if McKay was annoyed that they were going to this much effort for the former baker after what he'd done to them.

When he heard the sound of men charging into the village, he was almost grateful for this further evidence that his theory had been correct; at least he wouldn't have to put up with any more of Lucius's stories (Which were starting to become both repetitive and formulaic; the man always seemed to 'forget' something that they had to ask him about).

"What-?" Lucius began, halting his current story as he looked sharply over at one window as the sound of gunfire filled the streets outside.

"Wait a minute…" McKay said, looking at John with a new sense of apprehension as someone started yelling from the street, the villagers in the room heading out amid Lucius's platitudes that he'd be with them soon. "Am I getting paranoid, or was that-?"

"_Don't_," John said, his eyes narrowing as he heard the same voice that McKay was about to name.

He'd forgiven the Wraith that this bastard had used against him for his crimes, but the thought that he was on the same planet as Kolya again was not inspiring thoughts of forgiveness.

Right now, John wasn't sure if he wanted to gut Kolya for nearly killing Elizabeth during that long-ago siege of Atlantis or for what he'd done to him during their last meeting, but either way, the bastard was going down…

"_No_," a voice suddenly interjected; John only realised when he looked down that Teyla had grabbed him by the wrist and was looking at him in a very firm manner.

"'No'?" John repeated, looking at the Athosian woman incredulously. "Do you _know _what that bastard-?"

"I am fully aware of what he has done to us in the past, just as I am aware that we are not… prepared to make a stand at this time," Teyla said, looking pointedly at John despite the glance at Lucius showing that she was remembering to keep his identity secret. "If you attempt to go out and confront the Genii, we are all aware that Kolya and his men are prepared and willing to burn down this town out of spite if we deprive them of a direct fight, and we are not equipped for the kind of confrontation you are used to."

"She's right," McKay said, shooting an anxious glance at Lucius for a moment before he focused on John. "I mean, you did great in Atlantis, but we just don't have the home-field advantage here; you don't _know _where to go like you would there…"

As much as John hated to admit that he couldn't do anything, he had to admit that his team had a point; there were too many innocent people at risk here for them to just go in and start shooting at the enemy, and he didn't have the home field advantage like he had the last time he'd fought them during the invasion…

Glancing over at Lucius, John was only partly surprised to see the other man walking towards the door; Lucius might be an idiot and a coward, but he _did _have an ego that wouldn't have been helped by that force-field.

"And where are _you _going?" he asked, walking over to slam an arm over the door before Lucius could walk through it.

"To deal with the attackers, of course," Lucius grinned. "After all, I'm the hero-"

"You're the _idiot_," John said firmly. "You think that just because you read a few files you know anything about the Genii?"

"I read _everything_ in the files-" Lucius began.

"Firstly, you couldn't have read _all _of them, and secondly, if you go out there and they can't hurt _you_, they'll burn down the town around you out of spite," McKay said firmly.

"They're petty like that," John confirmed before Lucius could say anything himself. "If we go out there without a plan, people are _going _to get hurt."

"Killing all of them isn't a plan?" Ronon asked.

"We will not endanger these townspeople by engaging in a fight in unfamiliar territory," Teyla said firmly. "If we can hide away until they have completed their search and failed to find us, then they will simply move on."

"Call it… strategic concealment?" McKay suggested awkwardly, as John turned to look at him. "I mean, I get that you don't _like _that plan-"

"I spent two years hiding in what should be my home because I had to," John said, staring at McKay for a moment before he sighed. "But… so long as it's only a short-term option… I can work with that."

"Well, if you need to hide, I _do _have just the place," Lucius said, walking over to a nearby grandfather clock and adjusting the hands to reveal a secret room behind a hidden door just to the side. "See, I like to entertain-"

"_Don't_," John said, not wanting to think about what Lucius might have used this room for as he walked into it, the rest of his team behind him before he turned back to Lucius. "Just go out there, tell them we've moved on, and agree to anything if it gets them to leave without hurting anyone; this is _not _a good time to be a hero, understood?"

"Of course," Lucius smiled, before he closed the door behind them, leaving John to sigh as he glanced over at the others.

"He's going to do something stupid," he said firmly.

"What makes you so sure?" Ronon asked. "He's dumb and arrogant, but he's also a coward-"

"Who hasn't encountered a problem that shield couldn't solve for him since he started using it," John noted, shrugging off his flak jacket to remove a small pouch he'd hidden underneath. "In other words, unless the guy's more competent than we think, he's going to do something arrogant and stupid that will put himself and possibly everyone else in this village in danger, so I believe we're going to need this."

With that said, he unfolded the pouch to reveal that it was the cloak he commonly wore as the Phantom, along with his own Ancient shield device and a flattened piece of metal.

"What's-?" McKay began, before John placed a couple of fingers on the metallic object and it suddenly sprang upwards into the shape of the Phantom's mask. "You made a collapsible version of that thing?"

"I realise that we want to establish distinct situations where John Sheppard or the Phantom are needed, but I also realised that it was always possible that one might turn into the other, so I thought it best to be prepared," John explained, as he reached up and tore off the strips of make-up concealing his injuries; he'd worry about reapplying them later. "Considering the numbers we're up against and Kolya's history with me in the mask, I think we can all agree that this is one of those times; this is just metal, since I couldn't incorporate all my additional extras and still make it easily portable, but it should be enough for our current purposes."

"I thought we agreed that going out to confront him directly is a bad decision?" Teyla said in a very pointed manner.

"It's a bad idea for _us _to go out there," John corrected her, as he rolled down his BDU sleeves. "Your argument about the tactical situation not favouring a standard ground confrontation is accurate, but that's only if we go out as we are and give the Genii new enemies to kill; if the Phantom goes out on his own, Kolya's own pride will demand that he faces me directly after I stopped his attempt to take Atlantis."

"Sounds like a plan," Ronon confirmed, nodding at John in approval as he shrugged on the cloak and checked his clothing; so long as he kept moving and removed the mission patches, nobody should be able to look closely enough to see that he wasn't quite wearing his usual outfit, and he still had his gun in a holster anyway. "What about us?"

"Stay hidden and help me keep things contained," John clarified grimly as he placed the mask on. "These people might not be the sharpest tools in the shed, but they don't deserve to suffer for Lucius's mistakes."

"We are _meant _to be a team-" Teyla began.

"And we still are," John said, nodding warmly at her as he made sure that his cloak and mask were secure. "Just trust that I know what I'm doing right now…"

* * *

As he crawled along the village rooftops, John wasn't sure what was more surreal; doing something like this after almost three years of sneaking around Atlantis, or doing this kind of thing in daylight as opposed to his usual preference for the darkness. His costume was a bit more basic than his usual attire, and he felt somewhat limited without his usual sword, but he had his gun and his training; with the aid of the rest of the team, that would have to be enough.

Besides, as much as he'd enjoyed his training back on Earth, it was good to remind himself that he hadn't lost his touch for fighting solo as well…

Reaching the area where he could hear the Genii soldiers talking, John wasn't surprised to see that Lucius's hair was wet as though he had been dunked in the nearby bucket of water; he knew from experience that the shield couldn't retain its own air supply, even if it would prevent toxic gases getting at the wearer. With Kolya facing Lucius while one of the mercenaries John and Ronon had spotted earlier stood beside him, it wasn't hard for John to work out what must have gone down.

"…already guarding the gate," Kolya was saying as he glared at Lucius. "I'll ask you once more; where are they?"

"I don't know," Lucius protested. "I don't!"

John hated to admit it, but on some level, he had to give Lucius credit for not selling them out straight away. The man was probably smart enough to realise that he was screwed either way, but he could have spared himself the torture if he'd just talked…

"KOLYA!" he called down to the Genii leader, standing up to his full height as Kolya and his men spun to look at him.

"_You_," Kolya spat, eyes narrowing as he glared at John.

"Me," John replied, smirking as he looked at the man who was rapidly becoming the Phantom's first real human adversary. "I understand you're looking for the Atlantis expedition?"

"I'll take what I can get," Kolya growled, before he raised his gun and aimed it at John. "_Fire_!"

As the Genii opened fire on John, he couldn't help but smile as his Ancient shield device casually absorbed and deflected all of the bullets being unleashed against it, each blast dissipating against the shield until his opponents had run out of ammunition.

"My turn," John replied, drawing his energy pistol and firing a quick series of blasts at the nearest Genii before he turned and ran along the rooftops, smiling as Kolya yelled for the men to follow him. At that distance, with Genii so close together, his gun didn't have the power to effective stun every one of his adversaries before they could draw another weapon, but by provoking them into going after him, he had a chance to turn this situation against them. Pausing as he ran only long enough to fire off another shot or two at his pursuers to keep them enraged, he kept on leaping from rooftop to rooftop until he finally came to the town's central square, leaping into the air and hitting the ground with a role that worked with the shield to help limit any damage he might have sustained in the impact.

As soon as he was back on the ground, John turned around to completely face Kolya and his men as they charged into the square. While Kolya and a few of his men were leading the charge, John noted that a few of the soldiers were clearly lagging behind the rest; Kolya might have talked about how he 'had' to be a fake Phantom if he was working with the expedition over natives of this galaxy, but clearly he hadn't been able to sell everyone on that idea.

"All this for me?" John asked, deciding to go with straightforward confidence and hope for the best; he was used to being in control of a situation, and he'd certainly dealt with these kind of numbers in the past, but unlike then he now had to worry about other people and didn't have the advantage of darkness.

"You deserve every _moment _of the pain that we shall inflict upon you for your sins," Kolya practically spat as he glared at the man in the mask. "You proclaim yourself to be our hero while acting against us-"

"If you think the Phantom is 'yours', Commander, you're even more demented than I believed you were," John said, staring grimly at his first true human adversary. "In all my life in this role, I have never claimed to be anything other than what I am; I defend the Pegasus Galaxy from those who would threaten it… and your efforts to take the power of Atlantis for your own ends will benefit nobody but the Genii. The expedition might not be _from _this galaxy, but I have more faith in _their _ability to use its technology than I have in yours; the fact that you don't agree with my view doesn't make me wrong."

"You-!" Kolya began, reaching to his side to draw his pistol, only for John to draw his energy weapon and shoot before the Genii leader could do more than touch the weapon. The blast not only shattered Kolya's gun, but also virtually disintegrated his hand, leaving him flying on the ground screaming in pain as he clutched at his cauterised stump.

"Ask yourselves this," John said, turning his attention to the Genii soldiers assembled around him as they took a moment to stare at their leader in shock. "Do you really think that you can draw your weapons before I do the same thing to any of you? And can you be sure which one of you I'll target if I _do _decide to shoot?"

"And can you be sure what _we'll _do?" a voice called out from the roof behind John. Under other circumstances, John would have cursed McKay's attempts to sound macho, particularly when he had such an obvious tremor in his voice, but under the current circumstances he'd take what he could get if there was any chance to limit the amount of people he'd have to kill to end this.

"Exactly," the masked man said, deciding to follow up on McKay's unrequested addition to the conversation. "You've lost the upper hand, your leader's incapacitated and has literally lost _his _hand, and if you start a fight, we have the high ground and at least some of you won't live past the next few minutes; if you all surrender, we'll put in a good word for you back with the Genii."

After a few moments, the stand-off concluded when one of the Genii dropped his weapons, with the rest of the team following his example.

"Good call," John said, nodding at them in approval before he walked over to crouch down beside the crippled Genii leader. "I suppose it's too much to hope that this has taught you a lesson or two about trying to tangle with me?"

"I _will_… find you…" Kolya spat, eyes narrowed as he glared at John despite the pain he must have been feeling from where his hand used to be.

"I'm sure you will," John replied, nodding briefly at his foe's stubbornness before his eyes narrowed. "But just remember; I only spared your life this time because I'm trying to be better than you. Keep pushing me, and the next time we fight, I may target something more vital to keeping you alive than a limb."

Maybe he'd regret not just killing this guy when he had a chance later on, but considering that Kolya was going straight back to the Genii after Atlantis had made the necessary arrangements, he felt that this was the best way to show their still-tentative new allies that they were trying to respect the Genii's right to deal with prisoners in their own way.

As for Lucius…

John smiled at the thought as the rest of the Atlantis team gathered around the disarmed Genii and prepared to lead them to whatever location the village had to offer that might serve as a jail for the next couple of days.

Considering that the guy hadn't just given in and given them up the second Kolya started torturing him, John was going to give Lucius some time to make an impression on the locals without relying on his shield device or similar systems before he tried to make the guy leave.

On the other hand, if he had _any _reason to believe that the guy was abusing his role as the hero again, he was going to come down on the bastard like a ton of bricks; just because he was trying to be less 'lethal' now that he was an official member of the expedition didn't mean that he had to give everyone a chance.

With that decision made, John turned around and headed back for Lucius's house; if he could change back before any of the villagers had the chance to see his face, he should be able to stop anyone else from learning that the Phantom had been here in the first place. After that, all that was left for him to do was give Lucius one last stern warning before he moved on to get these Genii prisoners back to their people, and this mission should be another success.

* * *

AN: So, what do you think of this particular twist regarding Kolya?

Trust me on this; John's decision here is going to have _very _interesting long-term consequences…


	9. Exploding Tumour

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: And here we are with the events of 'Sunday'; hope you enjoy the results

Clash of the Phantoms

Sitting in her office, Elizabeth had to wonder what she was actually going to do with this day off.

She'd issued it with the idea that the crew deserved the chance to take a break after they'd spent so much time adapting to life back in Atlantis after the Ancients were killed by the Asurans- to say nothing of the military staff having to adapt to John as their commanding officer rather than Sumner- and Heightmeyer had only confirmed the merits of the concept during a recent conversation. After the _Orion _had arrived in orbit for its latest supply run, Elizabeth had talked the matter over with Dixon and everyone had agreed with the decision.

Actually, Elizabeth had been particularly touched at the news that the Taranian and Athosian members of Atlantis and _Orion_'s crew had chosen to spend their time in the city as well as visiting their own people. While the Athosians were content with their new settlement on the tentatively-named 'New Athos'- even if Elizabeth still felt they should have been more annoyed at the Ancients basically kicking them off-planet like that- the Taranians were taking advantage of the _Orion_'s presence to have various equipment sent to them so that they could establish a colony similar to what they'd had on their home world. They obviously couldn't rebuild the force-field that the Taranian settlement had used originally, but Norina was working on creating a substitute using solar radiation as an alternative energy source. The Taranian scientist acknowledged that it wouldn't be as powerful as the original shield had been, but it should be enough to protect her people from a Wraith attack long enough for them to evacuate through the Stargate before it could break down…

And thinking about worst-case-scenarios was _not _going to help Elizabeth relax; she couldn't order the rest of her city to take time off and not do it herself.

The only problem was that the thing she most wanted to do was the one thing she couldn't _let _herself do.

As much as John Sheppard continued to… capture her interest… even after so many of his secrets had been revealed, she was fully aware that she just… wasn't likely to do the same for him. After all, John had originally met 'her' when she was an eighty-year-old woman shortly before 'she' had died of old age; that kind of revelation had to have _some _kind of impact on how she looked to him…

"Hi," a voice said, interrupting her train of thought. Looking up, Elizabeth saw a good-looking man with a beard in a casual shirt and trousers; she quickly recognised him as Michael Branton, one of the newer additions to the Atlantis Expedition, specialising in interfacing Earth's computers with Atlantis's own systems.

"Hi," Elizabeth said.

"What, uh, what are you doing here?" Branton asked.

"I work here," Elizabeth said, smiling at him despite the strangeness of the question/

"But it's our day off," Branton noted.

"Well, shouldn't _you_ be enjoying your leisure time, then?" Elizabeth countered, cursing the childishness of the response as soon as it left her lips.

"I got a little behind on my research this week," Branton said, indicating the control room. "Just wanted to drop off some results for the next Earth transmission."

"Great," Elizabeth said, as she turned back to the computer. "Good."

"I was thinking about grabbing some food," Branton continued. "Care to join?"

"I can't," Elizabeth said, awkwardly indicating her laptop. "I've got…"

"You're not capable of having lunch?" Branton interjected.

"Yes, I'm capable," Elizabeth said, smiling despite herself.

"Are you planning on eating today?"

"Of course."

"Great," Branton smiled. "Eat with me."

"Look," Elizabeth said, settling for the more publically 'acceptable' explanation for her reticence, "it's nothing personal, but… I make it a point to not have relationships with people who work for me."

"I don't work for you," Branton noted.

"I'm your boss," Elizabeth countered.

"Well, you're my boss' boss, actually," Branton smiled.

"Still, however indirectly…" Elizabeth began.

"Yeah, but with that thinking, everyone on this entire planet works for you," Branton said. "You're not gonna be friends with any of them?"

"Friends is one thing," Elizabeth said, turning back to her laptop to try and avoid this increasingly awkward conversation.

"Oh, you think…" Branton began. "Oh, wait a second, I see what's happening here; you think I'm asking you out on a date."

Elizabeth simply let the other man talk, even as he moved over to sit down opposite her on the other side of her desk. "No-no-no-no, this isn't a date, this is… this is lunch. This is the mandatory refuelling of our bodies. This is putting food in your mouth and chewing it and having something more engaging than a wall sitting across from you. That's all it is."

Despite herself, Elizabeth had to smile at his awkward manner of trying to dismiss her 'concerns'; she wasn't totally convinced that even he was buying his impromptu 'excuse', but he made a valid point about the need for something more interesting than a wall as she ate if she accepted his offer…

"You are more appealing than a wall," she confirmed his initial awkward question in the most neutral manner available to her.

"Great," Branton said as he stood back up. "Now, what say we grab some grub?"

"I still have an hour of work to do, and then…" Elizabeth began.

"Another hour, then," Branton smiled. "I'll see you in the mess hall."

As he walked out, Elizabeth wasn't sure how she should feel about what she'd just done.

Branton had made a valid point that he wasn't _directly _under her authority, as she just advised McKay on what she wanted the computer science teams to do and then he passed the orders on, and she had to make _some _effort to move on from the impossible emotional situation she found herself in, but this was still a bit of a questionable way of doing it…

* * *

An hour or so later, having 'cancelled' her original plan with Teyla, Elizabeth had changed into a slightly more casual top and gone down to the mess hall, uninterrupted apart from a brief conversation with Carson Beckett about his own planned day off for a fishing trip, all the while hoping that she wouldn't run into John at an awkward moment; this situation felt strange enough without her being faced with the _reason _it felt strange.

Branton had been right that this didn't have to be a date, and it wasn't as though she could ever have an actual _relationship _with John… but that didn't mean that she felt entirely 'right' about this. As much as she knew a relationship with John beyond friendship was an impossibility, it was still hard to completely ignore the _desire _for something more regardless of how impractical it was…

Shaking that thought off as she settled down for lunch, she had to admit that she enjoyed the casual conversation; after so long focusing on matters of business and the complications faced in running this city, it was actually a relief to have a chance to discuss more personal matters. The conversation about their favourite films had been slightly unusual- she'd never seriously thought about _When Harry Met Sally_ as a 'remake' of anything, and she just felt that _Annie Hall _took excessive pleasure in making things complicated- but even if she disagreed with the idea that men and women couldn't just be friends, she wasn't going to turn down a chance to have a good meal somewhere more appealing than the mess-hall.

She was almost disappointed that she'd never thought about some of the city's exterior areas as a location for a picnic; she supposed she'd grown so used to thinking of the outside as just somewhere for her to talk with John that she found it 'odd' to think about using it for more conventional purposes.

"It really is beautiful here, isn't it?" Elizabeth said, staring out at the open ocean.

"Yeah," Branton said, as Elizabeth took a last sip of her bottled water. "All done?"

"All done," Elizabeth confirmed with a brief glance at her bottle.

"I guess lunch is over," Branton said.

"I guess it is," Elizabeth said, as she put the bottle down.

"Should have brought dessert," Branton mused. "Would've lasted longer."

"I really should get back anyway," Elizabeth said, lost for a better way to get out of this suddenly awkward moment

"What are you doing tomorrow?" Branton asked.

"Mike…" Elizabeth began.

"Look," Branton said, leaning in to talk to her in a lower voice, "I like you, and I'm extremely charming; I'd like to see you spin those into negatives."

The problem was that the only negative Elizabeth could immediately come up with was a very simple one that she couldn't express; no matter how charming he was, Mike Branton would never be John Sheppard.

"Mike," she said, looking firmly at him to limit the possibility of him misunderstanding what she was about to say, "this has been an… interesting time, but-"

"Oh, don't say 'but'; I _hate _'buts'," Branton said, rolling his eyes in frustration.

"This might be cliché, but it's not you; it's me," Elizabeth said, deciding that she might as well be reasonably honest with him even if she couldn't share everything. "It's just… to be completely blunt, I'm still dealing with how I feel about someone else, and it wouldn't be worth your time to get caught up in my mess."

"And what if I think your 'mess' would be worth it?" Branton asked. "Life needs a little interrupting every now and then-"

"You can't just 'interrupt' how I feel and expect things to work out," Elizabeth countered, shaking her head in frustration. "I shouldn't have done this; I thought-"

The sound of her radio gave her a welcome opportunity to withdraw from this conversation before it could get any more personal; whatever anyone else had to tell her, it couldn't be more uncomfortable than this meal had just become.

* * *

Hurrying up to the main tower, John had no idea what he expected to find or what he'd actually do when he got there, but in a strange way, it had to be easier than whatever was waiting for him back in the training room.

He'd hoped that he could reassuring Ronon Dex's remaining concerns about his appearance by training with him, but no matter how much control he demonstrated, it seemed as though Ronon was still waiting for him to slip up and demonstrate the trademark Wraithspawn psychopathic 'urges'. He could take a degree of comfort in the fact that Ronon had felt comfortable enough to tell him that he'd been married back on Sateda, but that still left a long way for him to go before the other man felt comfortable treating him as anything other than a colleague.

He appreciated that his face would never make it easy for him to make friends with Pegasus natives when their default response to seeing something like him was to run away before it tore them to bits, but Ronon and Teyla had known him as the Phantom; couldn't they just accept that he wouldn't snap just because they could see what was under the mask now?

As he arrived at the site of the explosion, John tried not to wince at the scale of the damage before him; even after everything he'd done as the Phantom, it still hurt to see Atlantis sustain this kind of damage. He briefly registered Beckett and his team taking Teyla away with a large piece of shrapnel sticking out of her side, but as much as he tried to consider the Athosian a friend, he only had one priority right now…

"What the _Hell_ happened here?" he said, looking urgently at Doctor Radek Zelenka as the Czech scientist removed a breathing mask from his face while studying a warped wall that must have been at least close to the source of the explosion.

"There was an explosion," Zelenka said grimly.

"That's obvious; the question is _how_?" John asked urgently. "Atlantis doesn't just blow up after thousands of years!"

"I'm still working on that," Zelenka explained. "I wasn't allowed on the scene until the emergency crews cleared the floor; what took you so long?"

"Transporters are down and there were a lot of stairs to climb," John said, indicating his own more casual attire in the process; he still wore the mask for comfort's sake, and kept a couple of small items in his pockets in case of emergencies, but now that he didn't need to hide all the time he'd stopped carrying some of his equipment around Atlantis, simply wearing the usual black BDUs of the rest of the Earth expedition. "Do we have _anything_ on what caused the blast… and what are the casualty figures?"

"Three dead and a dozen wounded," Zelenka explained. "McKay called earlier to say that he thought he'd found something in his lab, but he wouldn't share the specifics. The good news is, though, the structure is intact, so there's no danger of the tower falling down. There _is_, however, something very odd."

"Specifically?" John asked.

"According to our eyewitness reports, this was caused when Doctor Hewston just… blew up."

John blinked.

_Blew up_…

His blood ran cold at the thought.

He'd read a few notes about some of the Ancients' more questionable projects, but he'd really hoped that they'd destroyed that thing after the disastrous results of the original experiment…

"No trace of explosive residue, right?"

"Well… no, actually," Zelenka said, looking at John in surprise. "Do you-?"

"I have an idea," John confirmed grimly. "Looks like Hewston stumbled across something I _really _thought the Ancients would have destroyed earlier…"

He trailed off as a horrible thought occurred to him; he didn't know how long that device took to _create _the tumours, but he was fairly sure that Atlantis protocols wouldn't allow scientists to go around examining unexplored laboratories on their _own_…

* * *

"Explosive tumours?" Elizabeth repeated, wondering if she'd jinxed herself when she'd wished for something to distract her from the awkwardness of lunch as she looked at John, who'd clearly gone all-out to reach her office after his initial investigation of the explosion.

"From what I found in the city's archives, it was one of the Ancients' less successful anti-Wraith weapons," John explained grimly. "It basically operates by generating a unique form of irradiated particles that have been genetically programmed to enter the humanoid system and gather behind the lungs, collecting various trace elements from the body to create an explosive compound that manifests as a tumour and explodes."

"But they never used it?" Elizabeth asked uncertainly.

"Couldn't work out how to make the irradiated particles only form in the Wraith," John confirmed. "I thought they'd at least destroyed the prototype after the initial experiments, but they must have moved it to one of the outer labs I never got around to investigating…"

"You can't blame yourself, John," Elizabeth said, looking at him with that same casual smile that somehow always made John feel better. "You had a whole city to yourself and a lot of things to deal with; nobody expects you to have catalogued _everything _in it."

For a moment, as John exchanged a grateful smile with Elizabeth, he could almost imagine that everything was normal…

"_Elizabeth, are you there_?" McKay's voice suddenly said over the radio.

"Rodney," Elizabeth sighed as she activated her own radio in response, "if this is about the explosion, John already told me about the possible source-"

"_He knew about the tumours_?"

"_You _know about the tumours?" John interjected, grabbing the radio from Elizabeth.

"_You're there_?" McKay asked in surprise.

"I was just telling Elizabeth what I'd found in the archives; do you know if anyone was with Doctor Hewston when she might have been exposed to the device?" John asked urgently.

"_I was… just about to ask Elizabeth to start organising a search for Doctor Watson, actually_," McKay admitted, tone clearly uncomfortable at the developing situation. "_He was with Doctor Hewston when they found some kind of machine that generated irradiated particles last night, but it didn't seem that serious at the time_…"

"Damnit…" John groaned, shaking his head in exasperation.

"_Let me try this_," McKay said, with a moment's pause being followed by another call. "_Doctor Watson, Doctor James Watson; report your whereabouts immediately_."

"Citywide broadcast?" John said, looking at Elizabeth in surprise.

"The advantage of being in an official position," Elizabeth smiled at him. "You can delegate that kind of authority-"

"_He's in the infirmary_!" McKay yelled anxiously over the radio, interrupting their conversation. "_I'm trying to call Carson_-"

"On it!" John confirmed, charging out of the office and heading for the infirmary as fast as he could. "Get an ordinance disposal team down there; I'll see what I can do!"

Watching John run from the office, Elizabeth privately cursed this fresh reminder of what had attracted her interest in John in the first place; he always dived into action if it would give him a chance to save others, regardless of the risk to himself.

Unfortunately, that was the main reason she knew it wasn't worth pursuing a relationship; could he ever show that kind of… commitment to a single person?

* * *

Even as he ran from Elizabeth's office, John acknowledged that he didn't really _know_ how long he had until the second tumour exploded, but at least he knew where he had to be if he was going to do anything; he might not have his old array of gadgets, but he could at least move fairly quickly when he didn't have to worry about being caught.

After a few moments of rapid running through the corridors, he finally reached the infirmary level just in time to see various infirmary staff hurrying out of the room in question.

"What's going on?" he asked, grabbing the arm of a nurse he recognised as one of Carson's most regular assistant nurses.

"Doctor Beckett ordered us out of the infirmary while he's trying to extract that… explosive tumour thing!" the nurse said, looking anxiously at John. "Can you-?"

"I'll do what I can," John nodded, hurrying up to the locked infirmary, waving a hand over the control panel, only to find no response.

"Damnit…" he groaned, slumping against the door. He might have installed various security codes in the city to help him access most locations in an emergency, but as part of his new official role in Atlantis, he'd been forced to give certain members of the senior staff the ability to override those codes in cases where they had a more specialised view of the situation.

He wanted to respect his new colleagues' rights, but this kind of thing was a clear example of why he'd preferred acting on his own…

"_This is Doctor Beckett_," Doctor Beckett's voice said over the radio. "_I've extracted the tumour, and I'm opening up the O.R. level_."

"Great," John said, smiling in relief as he heard one of the side doors open in the infirmary through the main door. "Just hold on, and the disposal team should be there soon."

"_OK_…" Doctor Beckett said, before sounding frustrated at the other end of the radio connection. "_Damnit; I'll meet them halfway_."

"Hold on!" John began, heading for the main door once again, relieved when it opened after the initial lockdown.

"What-?" Doctor Beckett said, turning to look at him in surprise. "What are _you _doing here? I thought you'd understand-"

"I get that I can't do anything right now; I just thought I'd make sure that you had a good chance of getting out yourself," John said, reaching into his pocket and tossing his shield device to the doctor. "It's been configured for your use; wear it."

"Wear it?" Carson repeated, looking at it in surprise. "But-"

"Even if you can get this tumour to the disposal team in time, there's no way to be sure how explosive this thing is going to be," John said grimly. "I can't stop it exploding, and I think I know you well enough to know that you're not going to abandon this if you have a chance to save someone, but I _can _make sure that you've got enough of a chance of surviving that blast."

"…Thanks," Beckett said, clipping the device to his chest before he turned back to the small box he'd been carrying earlier. "You'd better move; I have to focus right now."

"Right," John nodded, moving back towards the door. "Good luck."

"Always appreciated," Beckett said as he picked up a scalpel just as John left the room.

"_You're _leaving _him_?" McKay said incredulously over John's earpiece. "_If that thing goes off_-"

"I can't contribute anything to getting that tumour to safety, and I think we all know Doctor Beckett well enough to know that he's not going to leave a patient if there's still a chance to save him, and Elizabeth and I don't have the authority to countermand his orders in a medical situation," John explained solemnly. "I've done what I can to help him."

"_How_?" McKay protested. "_We don't know how long that thing has until it explodes; Hewston was contaminated at the same time and she exploded before him_-!"

"We have to have faith," John said firmly. "There's nothing else we can do about it right now."

There was nothing that anyone could say to that statement, so John simply stood outside the infirmary in silence, waiting for a few moments for any sign of the disposal team or Doctor Beckett finishing the operation. This might be a risk, but as he'd said earlier, he had to have some faith that the rest of the expedition knew what they were doing, or he wasn't going to get anywhere continuing some variation of his 'lone wolf' crusade which had only managed to take him so far before the expedition arrived to help him…

"_We just made the hand-off_-" Doctor Beckett's voice said over the radio, before a loud explosion filled the transmission, followed by a sudden silence.

"_Doctor Beckett_!" Elizabeth's voice yelled over the radio.

"_Carson_!" McKay called out anxiously. "_Carson, are you_ _there_?"

"_Fine_…" the Scottish doctor replied, his voice sounding shaken but otherwise unhurt. "_Took a few knocks… but the shield device… stopped the worst of it_…"

"That's… good to know," John said, even as he already knew that the disposal ordinance team probably wouldn't have been so lucky.

He'd done his best to limit the death toll, but he wasn't a god; there were times when all you could do was save one life and hope for the best.


	10. Under Pressure

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

Even weeks after the events of the explosive tumour crisis, John had no idea what he should feel about the more personal elements of recent events.

He might have managed to get through the actual crisis with the smallest possible amount of casualties after the initial tumour explosion- considering the scale of the blast, five deaths and twenty injuries wasn't that bad- but he was still troubled by the most personal revelation of that night.

Elizabeth had been on a _date_?

It might not have worked out, but the fact that she _could _do something like that had just reinforced how he couldn't even really try to 'move on' from his own feelings for her; even if he could consciously accept that she didn't see him that way, he doubted anyone would be willing to even date someone who looked like they'd come off the loser in a fight with a bag of wrenches.

People might say that it was what was inside that mattered, but no woman should have to put up with a face like _this _on a regular basis…

He was actually grateful when they were assigned to take a look at the underwater drilling platform some distance from Atlantis; he'd noted the thing during some of his searches of the city's archives, but with Atlantis's own power reserves more than sufficient he'd never felt inclined to take a closer look at it when the city itself had so much to capture his interest. It might put him in close proximity to Elizabeth- who had insisted on coming along to survey this new discovery even if she acknowledged that she couldn't directly contribute anything to the search- but at least it gave him something interesting to think about while 'flying' the jumper through the ocean to search for the station's precise location. McKay had a few comments to make in the rear whenever anyone complained about his inability to pin down the station's precise area, but John was actually glad to hear that; it gave him something to think about beyond his current personal anxieties.

It was just a pity that the rest of the team didn't share his view on things; even if he'd learned to tolerate that kind of discussion, it was still a bit irritating to hear McKay griping about the demands placed on his time when everyone else knew that he enjoyed being the go to guy for these kind of enquiries.

"Still glad you came?" John asked Elizabeth as the conversation in the rear turned to McKay's apparent confusion over the name of one of the other scientist he'd brought along on this expedition; however he felt about Elizabeth 'moving on', he didn't want to lose her friendship.

"Oh, sorry," Elizabeth said. "I was… preoccupied thinking about the geothermal drilling platform."

"We should be there soon," John said, reaching over to check the ship's scanners. "We just passed the thermal layer and I'm getting some readings a couple of hundred feet ahead."

"If we can find an alternate and possibly limitless power supply, that would make even this long search seem worthwhile," Elizabeth said. "Don't get me wrong, we appreciate your donation of your ZPM supply, but it's still limited given our inability to create or recharge them ourselves; geothermal energy might be complicated, but if it's something we could maybe recreate… well, that could be very helpful back on Earth."

"Fair theory," John nodded, just as the HUD activated. "OK, we're coming up on our target."

As the other scientists came up to the front of the ship, John smiled in approval as he took in the station ahead of them, the whole structure resembling photos he'd seen of oil rigs back on Earth, apart from a more complex 'control tower' at the end and a more unusual kind of docking system at the other. Its long-dormant systems were already responding to the 'command' of his Ancient gene, as lights came on and various other subtler computer programs were brought online, indicating a platform that seemed prepared to take the jumper if they wanted to dock.

Even as he moved the ship into position to one of the tunnels in the side, John tried not to wonder if they were about to discover some deeper reason why the Ancients hadn't gone back to this thing long ago…

* * *

"All systems are online and functioning at full capacity," McKay said a couple of hours later, laptops connected up to the various consoles in the station's main control room. It hadn't taken long for them to identify the station's central control area- it might be limited compared to Atlantis's, but it was also the only place here with any kind of computer in abundance- but Elizabeth was still cautious about what they might discover in this area.

"You mean we're generating power already?" Elizabeth asked sharply.

"Well… no," McKay replied. "No, but we probably could if we wanted to."

"No, slow down," Elizabeth said, holding up a warning hand. "The Ancients abandoned this project for a reason; let's try to find out what that reason might be _before_ we start drilling into the planet's crust."

"Yes, well, fair enough," McKay said.

"Quite," John noted, from his own position beside Elizabeth. "The last thing we want is some kind of real-world _Inferno_ project."

"Inferno?" Elizabeth asked.

"I had a couple of cousins in Britain who were big fans of _Doctor Who_," John smiled slightly. "One of their favourites was this storyline where the Doctor witnessed this attempt to tap geothermal energy that released some kind of strange gas that mutated everyone it was exposed to into… well, some kind of wolf-man thing is the best I can come up with."

"You _do _get that was only a kid's show, right?" McKay asked.

"With some interesting ideas; no reason to ignore the possibility because of the source," John countered, before he turned back to study the controls. "As Elizabeth said, there has to be _some _reason the Ancients decided not to take this project any further…"

"_Ronon Dex_," Ronon's voice suddenly announced over the radio. "_Everyone back to the Control Room; we might have a problem_."

It might be a potentially dangerous turn of events, but John sincerely hoped that whatever Ronon had discovered would explain what had prompted the Ancients to abandon this station in the first place…

* * *

"We did a complete life signs scan; it's the first thing we did when we stepped aboard this station," McKay said, looking tetchily at the Athosian woman who had apparently just detected a Wraith presence in the area. "Look, I promise you, there is nobody here but us."

"I know, Rodney, but I am sensing it even closer now," Teyla said, moving her head around in that manner he'd come to recognise as her trying to 're-tune' her 'gift'.

"Well… maybe it's the pressure," McKay said dismissively. "It's been known to do things to the mind."

"Check again," John said firmly, in a tone that wouldn't allow McKay to disagree. Swallowing slightly in apprehension at the stare John shot in his direction, McKay nevertheless turned around and activated the life-signs scanner once again.

"There," he said, turning back to John once the scanner had been triggered to show only the twelve people currently in the central control room. "All life signs accounted for; are you happy now?"

"Wraith don't show up on life-signs detectors if they're hibernating," Elizabeth noted.

"I know what I am sensing," Teyla affirmed apprehensively.

"There is no Wraith here!" McKay protested. "I'm telling you-!"

"Nothing _here_…" John said, holding out one hand as a terrible thought came to him.

"What?" Elizabeth asked, looking back at him.

"We know that the Wraith and the Ancients fought their last battle on this planet, right?" John said, looking between the rest of the assembled team. "And we know that Wraith can live a long time… so isn't it possible that a Wraith ship crashed here and at least one of its crew managed to survive until we woke them up by passing by?"

"You mean… like on that planet on the outer reaches of this system?" McKay asked, looking at him with a new curiosity. "You know, I've been meaning to ask since you started working with us officially; did _you_ kill that thing?"

"Stumbled across it when I was scoping out the solar system and was a lot more paranoid than I am now," John replied with a brief shrug. "That thing was hungry and tired when I went to that planet, and I'd kept my jumper's defences up; knocked him off-balance with a drone, cut his hands off before he could get over the disorientation and try to feed, and after that he was almost easy to take down."

"What are the odds of that being the case here?" Elizabeth asked, looking at John with a more commanding presence at the thought of a potential crisis.

"Depends on what survived the crash," John said. "The Wraith on that planet was just a standard warrior who lucked out on being woken up first and ate the rest of the crew to keep himself going, but anything that made it this close to Atlantis was more likely to be crewed by the elite…"

"In other words, if you're right, we'd be dealing with something more powerful and more dangerous than the standard Wraith no matter what survived the crash," McKay sighed. "Well, that's _all _we needed…"

"I can determine the truth easily enough," Teyla put in. "If I can reach out with my mind and establish a link…"

"Couldn't that be dangerous?" Elizabeth asked.

"If there is no Wraith, then there will be no mind for me to link with, and therefore no risk," Teyla explained rapidly. "But if there _is_ a Wraith nearby…"

"We need to know," Elizabeth nodded in grim understanding, before she turned to look at John. "Is there somewhere we could go for Teyla to establish a link in private?"

"Should be a few crew quarters down here," John indicated a nearby corridor. "This place was only ever intended to be a drilling platform; they wouldn't have wanted to make it difficult for the crew to get back to work if something came up."

"Fair point," Elizabeth nodded, before joining Teyla, Ronon and John as they headed towards the indicated corridor. A few moments later, Teyla was sitting on a bench in the middle of the room, her legs crossed and her hands held out palm-up as she prepared for what she was about to attempt.

"You ready?" John asked, looking anxiously at the Athosian woman despite the mask that concealed most of his features.

"I only require brief contact to determine if I am right or not," Teyla said, looking at John with a brief smile, her usual uncertainty about him forgotten. "I will be fine."

"Remember, just link up long enough to determine what we're dealing with should be enough," John said.

"And we'll all be right here to bring you out of it if things go wrong," Elizabeth added.

As Teyla closed her eyes, John exchanged a brief glance with Ronon, the two displaying their weapons to each other to confirm that their energy pistols were already set to stun in case of a worst-case scenario. Their focus soon returned to Teyla as she took a deep breath and concentrated, her hands moving to her knees as she reached out with her mind…

"Teyla?" Elizabeth asked, looking anxiously at the other woman as she finally opened her eyes.

"I-I was mistaken," Teyla said, looking slightly bewildered. "There's nothing there."

"Good to know," John said, even as he noted that down as something to be concerned about; even if he didn't _want _to have to face any Wraith that had survived this long, he doubted that Teyla's powers were something that could be 'tricked' by pressure like she was currently claiming…

"Well," Elizabeth shrugged as she stood up, "if there's nothing for us to worry about, we have a lot of exploring to do."

"'We'?" John repeated.

"Until Rodney delivers the preliminary status report, I'm all yours," Elizabeth smiled. "Put me to work, Colonel."

"Although, let's make up some time," John said, taking a moment to think about his best decision right now before making his mind up; regardless of his concerns about Teyla's senses, if there was a Wraith out there, it couldn't do anything to them when they were inside the locked drilling station. "Ronon, you and Teyla search that way, Elizabeth joins me in checking out the other side; we rendezvous back here in an hour or if we find anything interesting."

As Elizabeth followed him out of the room and down another corridor, John was already trying to figure out what would be his best plan for the current arrangement. Obviously, he wasn't going to bring up her 'date' no matter how much the experience had hurt him- if she wanted to go out with someone else, he didn't have any real right to object or feel hurt by it- but on the other hand, he didn't have any real evidence for his concerns about what might have happened…

"Is something wrong/" Elizabeth asked, after a few moments of silence.

"Just… Teyla," John said, lost for anything better to say as he looked at Elizabeth; after everything he'd shared with her when he was 'officially' Atlantis's 'most wanted', it seemed ungrateful not to tell her at least some of the truth now. "I get what she said, but I just can't share the idea that her gift to sense the Wraith doesn't really work in a manner that could let it be 'tricked'…

"You think she was lying?"

"I think there might be something else going on here…" John said, shaking his head as he looked around the corridor they were walking through. "I just don't know what; even if a Wraith crashed, it couldn't have gained access to this place while the whole facility was on lockdown…"

Further conversation ended when the lights in the corridor suddenly went off, prompting John to pull out his Ancient shield device and clip it to his chest.

"What-?" Elizabeth began, before the device began to glow with a low light.

"One of the alternative functions I discovered for this thing; on a low level, it can just serve as a kind of flashlight without needing to create a full shield," John explained. "Takes up less power and it's a useful little extra."

"Nice," Elizabeth nodded in approval, before she turned to activate her radio. "Rodney, what's going on?"

"_What do you mean, what's going on_?" McKay replied.

"We just lost lights in our section," Elizabeth explained.

"_What_?" McKay replied, followed by a brief pause before he continued, most likely checking something at his end. "_Huh, you're right_…"

"Can you clarify _how _that happened?" John put in.

"_No idea; we've just lost power to some forty percent of the station, including sensors_," McKay explained. "_Zelenka, what are you doing_?"

"_What do you mean, what am I doing_?" the Czech scientist asked as he joined the conference message.

"_Have you lost power where you are_?"

"_No; have you_?"

"_No_," McKay replied.

"Well, _we _have, and I want to know what's going on," John said. "Ancient tech of this quality doesn't just shut down after centuries of dormancy; we need to work out what happened here."

"_It's probably just a few operating glitches; I'll get the power back soon_…" McKay said in frustration.

"Ronon, Teyla?" Elizabeth asked, turning her attention to a different channel. "Report your position."

The lack of response was enough for John to know that things were going increasingly wrong; the only question now was whether it was something he could stop before it got any worse…

"McKay," he said, turning his radio back to the Canadian scientist, "we've lost contact with Ronon and Teyla; you have their position?"

"_No, internal sensors are out_…" McKay said, pausing for a moment before he continued. "_However, I _have _determined where the power went down; it's an auxiliary control area in search grid six, near where Teyla and Ronon were searching_."

"Right," John said, taking a moment to consider his options before making his decision; whatever was up right now, Teyla and Ronon almost certainly needed help, and he'd have time to determine if any of his worst-case scenarios were actually happening before even the worst of them became an issue…


	11. Death Underwater?

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

McKay and Elizabeth behind him as he approached the auxiliary control room that had been identified as the likely source of the current power cut, John wondered how long they had until whatever was causing this attack made itself known to them. He had a few ideas for what he was up against, but since most of them involved crashed ships during the last stage of the Ancient/Wraith War above Atlantis, he was _really _hoping that he was wrong; the last Wraith he fought in that state had been a nightmare to put down when he only had himself to worry about…

While John had a few doubts about McKay's plan to send some of the base staff to use the jumper's own sensors to check the base, he supposed that it was a fair enough decision based on what they knew. He wasn't going to get anywhere by starting a panic with a theory, and if a Wraith was out there, it was probably fairly weak by now no matter how careful it had tried to be with its available food supply. If they could just identify where everyone was, they could hopefully isolate any intruders in one part of the base until they worked out something better, and then they could focus on working out how to use this station and/or dealing with whatever was causing this blackout…

The sound of gunfire from up ahead cut John's train of speculation short, prompting him to draw his energy gun and his pistol and run towards the gunshots, Elizabeth immediately behind him as McKay followed just after them, vocally complaining but clearing willing to come along anyway.

The more John thought about this mess, the more anxious he became that he was dealing with something far more complicated than an old bit of technology having teething trouble…

When the three-man team went around another corner and found Ronon lying on the ground, John knew that they were in trouble; he'd seen Ronon in action enough times to be sure that he wouldn't be taken out by a simple accident.

"Are you all right?" Elizabeth asked, hurrying over to kneel down beside the Satedean as he groaned and tried to get up.

"Did you see who attacked you?" the expedition leader asked.

"Yeah, it was Teyla," Ronon replied grimly.

"Teyla?" McKay repeated. "Why-?"

"_Wraith_," John said grimly.

"Wraith?" Elizabeth repeated, before understanding dawned. "But we didn't detect anything when we ran our scan; how could something take her over-?"

"They're virtually immortal and fairly powerful, remember?" John noted grimly. "A few ships crashed into the ocean during the last battle, and I'm willing to bet that a Wraith or two survived until we came down here and started stirring things up; something strong enough to live this long could probably get into Teyla's head easily enough if she wasn't expecting it."

"And walk along the ocean floor without a pressure suit at these depths?" McKay put in.

"Again, the Wraith are fairly strong even when they're young; if something lived this long down here, it's probably worked out how to control its ability to cope with the conditions outside of its ship, even if it couldn't go anywhere useful without more help," John noted. "Take little trips out at a time to build up its endurance, and it might have even found a way to walk to this station, even if it couldn't get through the shields until someone turned them off."

"Good point," Elizabeth nodded grimly. "Doctor Beckett did speculate that they might even be able to survive in a vacuum so long as they weren't left out there for too long and had some kind of warmth nearby; compared to that, being underwater near thermal vents would almost be simple."

"And this didn't occur to you earlier because…?" McKay asked as he shot a pointed stare at John.

"Because I'm not some comic book character who plans for _everything_," John countered. "I can only work with what I've got, and what I had suggested that any Wraith out there would have done something earlier if it survived the crash or would have just died from the pressure down here; I can't be blamed for finding out that the ridiculously unlikely actually _happened_."

"Right," Elizabeth nodded in understanding at John before she turned to address the team. "In any case, our priority right now has to be to find Teyla and work out what she's trying to do; John, tell everyone to congregate in the central control room, and then help us find where she might have gone."

"Check," John said, reaching up to his mask to activate his new inbuilt radio. "John Sheppard to all team; we have reason to believe that a Wraith has made it into this drilling station- or is making its way here- and is likely to be very hungry. Travel in pairs and get to the central control room as soon as possible; in my experience, hungry Wraith can be desperate, but we don't know how long it's been since it last fed, so it might be slower than they usually are."

As he heard the rest of the team starting to respond to his order, he could only hope that it had been given soon enough to stop Teyla doing anything she'd regret when she came to herself…

"_This is Zelenka_," the Czech scientist suddenly said over the radio. "_Someone has just activated emergency forcefields throughout the station_."

"Can you get back to the control room?" John asked.

"_Most of us are here already; we just need to work out the best routes for the others based on __what is left accessible_," Zelenka replied.

"What's Teyla doing?" McKay asked, panting slightly as they ran along the corridor.

"Best guess; creating a suitable path for the Wraith and following it up by making sure that we can't do anything with the controls to stop her," John noted.

"Right…" McKay said, before coming to a halt at a junction in the corridor. "OK, I'll head bac to the control room; if we're being hacked, I'll need to be there if I'm going to counter it."

"I'll come too," Ronon said, grimly raising his gun. "Can't exactly leave you alone if there's a Wraith out here."

"Thanks," McKay said, giving Ronon a brief grin of thanks before the two men hurried down a corridor, leaving John to look at Elizabeth.

"If you-?" he began.

"I'm safer staying with you," Elizabeth said.

The simplicity of that statement, as though she was almost surprised that she needed to even say that much, meant more to John than any words could have expressed. Not bothering to reply, he turned around and continued down the corridor, keeping an ear out for both Elizabeth's footsteps just behind him and any sound of Teyla up ahead, until they arrived in what looked like an auxiliary control room of some sort, Teyla staring at the various broken control panels in front of her.

"Teyla?" John asked, relieved when she turned around to look at him in genuine confusion; at least he didn't have to worry about her still being under the Wraith's control.

"J… John?" she said, shaking her head slightly as she looked between him and Elizabeth. "Wh… what am I doing here?"

"I have a few ideas, but I'd like to check in with the team before we worry about that," John said, walking over to take Teyla's arm as he smiled reassuringly at her. "Come on; let's… get back to the control room, huh?"

God, he hoped he was wrong about what they were up against…

"Rodney?" he said, activating his radio once again as they walked. "We've got Teyla; how's things at your end?"

"_Not great_," the Canadian scientist replied grimly. "_We've not only lost several key systems, but the entire operating code's been scrambled; communication's gone, control crystals are blown, half the power's gone, and a series of emergency forcefields have been set up at various points throughout the station_."

"To give the Wraith easy access?" Elizabeth asked, keeping the radio on even as she looked at John.

"Most likely," John nodded grimly, before turning his radio back on. "McKay, focus on reactivating internal sensors and disabling the forcefields between us and the Jumper; if the station can't communicate with Atlantis directly, the jumper's our best bet."

With that said, he shut off the radio and turned back to look at Teyla. "Did you sense anything about the Wraith that was using you?"

"Y… yes," Teyla nodded uncertainly, pushing aside her obvious fear at the idea as she looked at John. "I believe that it is a Queen."

"A Queen?" Ronon repeated, tightening his grip on his own gun.

"Great," John groaned. "I _hate _those bitches…"

"So what now?" McKay asked.

"We track this bitch down before she can do anything too extreme," John said firmly, before looking awkwardly at Teyla. "Uh… until we know how much control she had over you…"

"I understand," Teyla said solemnly.

John hated this, but he had to be practical now that he was considering multiple people; if it was just him at risk, he might have been willing to let Teyla come with him, but with the rest of the expedition in danger he had to be cautious.

"OK," he said, looking over at the two women, tossing Elizabeth his energy weapon after resetting it to stun as he drew his own P-90, "I'm going to head for the jumper to make sure things are under control there; stay here and stay safe."

He didn't stop to say anything else before he charged down the corridor, hoping that his memory of the station's layout was correct and that the Queen hadn't blocked off every path just yet; she might be intelligent, but the Wraith couldn't have been inside this station before and Teyla's own memories wouldn't have been enough to cut _every _route off…

Despite having to take a few detours on the route between the back-up control room and the jumper's docking bay, with some shields raising and lowering as he ran through the station amid half-heard comments from the control room staff that they were working to shut all the shields down, it didn't take long for John to reach his destination. As he charged into the docking bay, he found himself facing the back of a Wraith Queen standing over the body of one of the scientists, another corpse off to the side.

"STOP!" John yelled, brandishing his P-90 even as he knew that it was too late to save the Wraith's latest meal. As the Queen turned around, John fired his gun at her, only for the Queen to dive out of the way before John felt a sudden pressure in his mind.

"Fascinating…" the Queen said, her tone the same chilling tone John had heard from other Queens as she stood back up. "You are… the Phantom…"

"Yeah, and you're… some lost Queen… who can't accept… that she got left behind," John countered, tensing his shoulders as he tried to maintain his hard-trained mental barriers. "Care to… make this easier?"

"I was about to make you the same offer," the Queen countered, chuckling as she flexed her fingers, clearly anticipating an additional meal. "You may have developed some reputation among my sisters' children, but I am not so pitiful as to fall-"

Seizing the moment, John pressed his finger down on the trigger, bullets erupting from the gun to strike the Wraith Queen in the chest. The blast only sent her staggering for a moment, but that was enough for John to fire another quick series of shots as she lost her grip on his mind, leaving her to fall to the ground as the pain overwhemled her.

"Got her," he said, turning on his radio as he checked out the area around the ship; there were two bodies lying on the ground, clearly the victims of Wraith feeding, but nothing else seemed to be damaged. "Two victims before I got here, but the jumper's structurally intact, and I've taken the Queen out."

"_She's dead_?" Elizabeth asked.

"Just out of it," John said. "I hit her with a few bullets, but considering what she's probably been through to get this far, her healing ability's probably been 'amped up' by feeding on her fellow Wraith; I didn't shoot at anything too vital, so she'll regain consciousness later."

"_Hold on; you're leaving her alive_?" McKay said over the radio. "_If it's a Queen, why not just kill her_?"

"Because Wraith don't live this long by being stupid, and Wraith Queens definitely don't get to their level of authority by charging into enemy territory without some kind of plan beyond killing everyone," John said firmly. "If she was smart enough to make Teyla set up those force fields and get down here in the first place, I want to be sure she doesn't have any other nasty surprises for us before I take her head off."

"_I thought you left your sword on Atlantis_?"

"My gun does the job well enough; I just find the sword neater," John noted, his gaze fixed on the Wraith. "Can someone get up here with the emergency sedatives and something we can use to tie this bitch down? In a situation like this, I think we can all agree that the more precautions we take the better."

"_We'll get right on that_," Elizabeth said, only a slight anxiety in her tone despite the thought of the threat they'd just confirmed was trapped with them. "_Keep an eye on her and we'll be there as soon as we can_."

"Check," John said, terminating the radio as he stared grimly at the still Queen.

He already had a few ideas about what they could expect from this mess, but the sooner he knew what they were up against for certain, the happier he'd be…

* * *

Staring at the Wraith Queen currently bound before her on the table of what seemed to be the station's equivalent of an infirmary, Elizabeth shuddered inwardly, both at the thought of what this 'woman' was capable of and what they had to do to prevent that. As much as she accepted that negotiating with the Wraith at present was a virtually pointless task, considering how much they enjoyed what they were and the various lessons learned from last year's aborted 'alliance' with Michael's hive, the concept of keeping prisoners like this still made her uncomfortable, particularly when they were having to resort to such extreme measures as repeated drugs to keep her contained.

She appreciated what the Wraith were capable of and acknowledged John's point that the Wraith would have just eaten the rest of the Geneva Convention if they'd been granted the chance to participate, but that didn't make it easier to countenance this kind of treatment…

"Welcome back," she said, controlling her reaction as the Queen regained consciousness and began to strain against her bonds; she trusted John's experience, but it still wasn't comfortable being this close to a Queen. "I trust you're comfortable?"

"That groggy sensation you're feeling are the sedatives we're pumping you full of," John put in firmly. "Just a precaution. As for the other precautions…"

Elizabeth gave John and Ronon a chance to demonstrate their weapons before she walked up to stand directly over the Queen. "Now then, you're going to tell us everything we want to know."

"In exchange for…?" the Queen asked.

"This is _not _a negotiation," Elizabeth said firmly.

"I disagree," the Queen said, grinning the usual sadistic grin of her kind.

"On what grounds?" John asked. "I'm fairly sure your ship's out there and you've been waiting down here ever since you were one of the unlucky ones during the Wraith's last attempt to blow up Atlantis, and you'd have come over here with the rest of your crew if you had any, so what we want to know is what you actually thought you were going to accomplish over here?"

"You are all going to die," the Queen said, ignoring John's argument as she continued to stare confidently at her 'interrogators'.

"We're at that stage already?" John said, shaking his head as he looked at the Queen. "You people have so little imagination…"

As the Queen defiantly turned her head away from them, Elizabeth didn't need her long experience with John to know that he was more unnerved by that last comment than he wanted to let on right now. Even if he genuinely wanted to believe that this Queen was just falling back on typical Wraith arrogance, they couldn't take the chance that it was something more…

* * *

"And we missed this earlier because?" John asked, looking pointedly at McKay after the scientist had revealed the results of his latest scans of the station's surroundings.

"Well, it's emitting very low EM results; add in the fact that it's partly buried in silt, and it's actually not that surprising that we missed it earlier," McKay explained, shaking his head in frustration as he studied the Wraith cruiser the science team had just discovered during the Queen's interrogation. "Still, if we'd just been paying more attention…"

"Nobody could have guessed that something could still be out there after all this time, McKay," John looked reassuringly at the scientist. "Like I said, even _I _didn't suspect anything until it was too late; we can't go kicking ourselves because of hindsight."

"So what now?" Elizabeth asked. "All that talk about our imminent death may or may not be an empty threat, but we have to find some way to be sure…"

"I can find that information," Teyla put in.

"Are you sure?" John asked. "That already went against you earlier…"

"She is heavily sedated, and this time I know exactly what I am dealing with," Teyla said firmly. "We have to know."

"OK," John said, nodding in thought. "I'll head out to see if I can find anything in the cruiser, while you get ready to see what you can get out of her if we need to get into her head."

"You sure that's safe?" Ronon asked.

"Hey, if I can knock her down, you can keep her down," John smiled at the Satedean warrior, trying to conceal his inner doubts. "Like I said during the interrogation, she'd have brought more warriors along if she had anyone else to do her dirty work; whatever's in that ship, I'm sure I've handled worse.

Maybe the Queen was just showing the typical Wraith arrogance, but when dealing with someone who'd managed to survive this long, John wanted to make sure they were covering all the angles, which included entering potentially hostile territory by himself to limit the risk.

* * *

As he cautiously moved the jumper towards the crashed Hive ship, John was grateful once again for the Wraith's typical arrogance; while the larger ships needed Wraith DNA to actually pilot them, most of the minor control systems were easy for anyone to use as the Wraith never expected anyone to try and break _in _to them. Setting the jumper down as close to the Wraith cruiser as he dared, John took a few moments to program the jumper's shield to extend from its rear hatch to the nearest entrance to the cruiser before he left the ship. It was fairly deep at this point, but after the time it had spent being protected by the station's own shield, the shield should still be good for an hour or so before he had to return to the drilling platform. Walking through the small ship, it didn't take long for him to reach the main control him, his eyes narrowing as he studied the Wraith's twisted equivalent of a command console.

His experience with the Ancient language might still be relatively amateur, but he'd learned enough to be sure that what he was looking at was extremely bad news.

"Damnit…" he muttered, before he activated his radio. "Everyone, I'm at the Wraith ship, and we have a problem; before she left, the Queen activated a self-destruct program set to go off in a couple of hours."

"_A couple of hours_?" McKay repeated. "_Why leave us so much time_?"

"She probably wanted to give herself enough time to get into the base and find a way out while underestimating our ability to hold her off; the 'why' of it doesn't matter right now," John said, his attention focused on the console. "What's important is that we need to shut this thing off before it blows up; if I remember the Ancients' records of this area, we're currently over a particularly thin part of the planet's crust, right?"

"_Which means that something the size of a Wraith cruiser blowing up in this area would release all that thermal energy to such an expansive degree that even Atlantis could be destroyed_," McKay finished, his tone clearly expressing his terror at the thought. "_Oh, that's _really_ not good…_"

"_Can't we just turn the self-destruct off_?" Ronon asked.

"With two hours to go and Wraith technology notoriously picky, I wouldn't like to try it unless I _knew _I had the right code," John said, staring grimly at the computer. "I just don't know enough about Wraith technology to know what would happen if I entered the wrong code; for all I know, the second I get it wrong I'd end the countdown and set it off now…"

"_I can find the code_," Teyla's voice cut in.

"_Teyla_?" Elizabeth said anxiously. "_You already_-"

"_I was caught off-guard last time_," Teyla said grimly. "_As we have already discussed, I now know what I am up against, and I know what I am looking for; I appreciate that you are concerned, but that will not happen again_."

"_And I'm here if things do turn ugly_," Ronon put in.

"Do it," John said after a brief hesitation, his guilt over what he was asking Teyla to risk only slightly appeased when Elizabeth gave the same order.

For the next few moments, all that John could do was stand anxiously over the control panel, listening to the silent radio connection for the next sign that anything was going to happen, wondering if he had enough time to try his luck if Teyla's current gambit failed…

When Teyla's voice came back over the radio to pass him the code, John grinned in relief as he tapped the necessary control panels, waiting for a few moments before the display for the self-destruct fell silent.

"It's done," he said, turning the radio back on with satisfaction. "Feel free to put her down."

"_With pleasure_," Ronon said, followed by the sound of his energy pistol discharging. "_She's headless_."

"Good," John said, looking grimly around the Wraith cruiser.

He was proud that he and his allies had managed to outmanoeuvre such an ancient Wraith Queen, but that didn't mean he was completely comfortable at the thought of staying in this ship any longer than he had to.

As far as he was concerned, the only thing they needed to focus on now was testing whether that geothermal drilling platform would be worth all the effort it had taken to get down here in the first place.

* * *

AN: A bit easier than canon, but with John's greater experience of the Wraith, it was easier for him to work out where the Queen came from and what she was after.

Coming up next is a more original chapter, as John considers recent events on a personal and galactic level while reflecting on his grimmer past as the Phantom


	12. The Phantom Who Came to the Party

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

Staring out at the city, the man once known just as the Phantom of Atlantis smiled slightly as he saw _Orion _hovering in position between two of the city's 'spokes'. The ship might have made significant progress since he had helped the Taranians start their work on it all those years ago, but since Atlantis became available, they were all still working on any way they could help it achieve its full potential, rather than the occasional improvisations they'd had to carry out. The salvaged _Tria _continued to be an asset in this regard, as parts of the more-damaged ship were added on to _Orion_, but it had still taken a while to completely finish the work. According to the science teams' analysis, the latest repair job should be all that was needed for the _Orion _to be restored to full working order, eliminating the last of the occasional glitches it had experienced up until now.

"John?" Elizabeth asked, prompting him to turn and look at her as she walked up to join him at the balcony. "What are you doing here?"

"Just thinking," John shrugged.

"When you could be down there celebrating the completion of one of the greatest feats we've accomplished over here?" Elizabeth asked, her expression half-teasing and half-serious as she indicated the _Orion_. "John, the only reason that ship's survived long enough to get this kind of refit is because of you-"

"And who do I appear as?" John countered, regretting his bitter tone even if he felt obligated to make his point. "The Taranians don't know that I'm the Phantom, remember?"

"Just because they don't know that you're the one in the mask doesn't mean you can't go down there in it," Elizabeth said, even as her sympathetic smile made it clear that she understood what was troubling him. It had been a difficult decision, but it had been decided that, like with the Athosians, only a few key Taranians would be told the truth about the Phantom's history once they'd determined who they could trust with such knowledge, to prevent the Pegasus natives accusing him of aiding them only to aid Earth; John didn't want to get bogged down in the task of reassuring everyone that he had been defending them for their own sake as much as protecting his own world. "Look, enough people in Atlantis appreciate the challenges of your position not to question you if you go down there as the Phantom; Colonel Dixon worked with SG-1 on enough occasions to understand when it's time to bend the rules."

Looking down at the grounded spaceship for a moment, John finally smiled in approval of Elizabeth's assessment. Even if he had agreed with the decision to keep his origins secret from most of Pegasus, there was no harm in confirming that he approved of what the Taranians had done with the _Orion_ since he met them.

Besides, on a practical level, he had to acknowledge that Elizabeth had made a deeper point than she realised; he might not want too many people to know that he was the Phantom, but that shouldn't stop him from going down to mingle with the general population of Atlantis and any visitors to the city as John.

He'd been an official part of the expedition for months; he needed to start using that for more than just issuing orders and knowing they'd be obeyed. He wasn't ready to go out in the mask for purely leisurely pursuits yet, but maybe he could stop in for a little chat…

* * *

It had never been a position he'd aspired to, but the more time he spent on the _Orion_, the more Colonel Dixon found himself enjoying the role. Once the Ancient gene therapy had been introduced to the SGC after they regained contact with Atlantis, all SG teams had been given priority in case they encountered any more Ancient technology, and while Dixon knew he wasn't up there with General O'Neill or John Sheppard in terms of the degree of control he had, he wasn't exactly a slouch either.

Getting the assignment to take the _Orion _had been a surprise, but Dixon had appreciated the reasons given for the decision quickly enough; they needed someone experienced with the kind of things that were out in the wider galaxy, without too many preconceptions about spaceship combat considering the unique nature of the ship. Once the finer details had been straightened out, he'd managed to convince most of the original Taranian crew to stay on board, and a few members of the Atlantis expedition had actually made a permanent transfer to the _Orion_, and he was proud to say that they'd all come together well, incorporating their contrasting experiences with the ship to create a very efficient system.

It was a bit difficult for him to find the time to make it all work while also spending time with his wife and kids, but he was looking into getting permission for his wife to be read into the program to let him talk with her more often when he was 'on duty'. He'd helped out SG-1 enough times over the years to have earned some favours from General O'Neill, and there was precedent for letting spouses know about the Stargate in exceptional circumstances, but it was still taking time for the fine details to get straightened out.

Still, for the moment, as he sat in one of the smaller buildings overlooking the pier that had become _Orion_'s unofficial 'dock' when it was at Atlantis, watching as his crew chatted with the Atlantis expedition, Dixon found it easy to forget about his own troubles in favour of appreciating why so many people had become so attached to this city since its discovery. The commute out to Atlantis in particular and Pegasus in general might be a long way, no matter what resources they acquired to improve their ability to travel via wormhole or upgrade their hyperdrives, but it was unquestionably worth it to take in all the sights at the other end.

The one thing none of the Earth members of the crew were happy about was the decision to maintain the illusion that John Sheppard and the Phantom were separate people, but even if Dixon wanted to believe that Norina and some of the Taranians would understand, he privately had to admit that it was best to keep something that big under wraps for the moment. With the Genii's response as an example of the most extreme possible results, Captain Alyssa Satterfield's tactical analysis had led her to express her concerns about how the Taranians might react at even a hint that the Phantom had helped them repair the _Orion _just for the expedition, rather than acting in his public role as the hero of the Pegasus Galaxy, so it had been concluded that it was easier to keep the secret.

Dixon wanted to believe that a few of the Taranians could be trusted with that knowledge, but it was better to wait and be sure than screw up and ruin their future relationships with some of their best allies.

That question aside, relations with the Taranians were progressing well, as they assisted the crew in understanding the ship while the SGC provided the Taranians' colony with support. A few geologists and biologists from the SGC had even moved to the planet to better study how the formations and life-forms they were familiar with from Earth had adapted to conditions in Pegasus since the Ancients came here. Relationships had been awkward at first, but Dixon was pleased at how few of the Taranian crew had asked to leave _Orion _for the colony. Most of them took their leave with their families, naturally, but for the most part, they were all settling comfortably into their new routines as part of the crew, offering some suggestions for where _Orion _might go on their next survey mission based on what they'd translated from the ship's database. They had taken to trying to search Atlantis's database using some of the access codes salvaged from the _Orion_'s old control crystals, but the codes only made it easier to refine their search parameters rather than making it easier for them to find everything. Most of the technology and resources that had been left in Atlantis had been identified by the man formerly known as the Phantom since he first arrived in the city, but Doctor Weir had confirmed that he'd only searched a certain area of the city around the central tower before concluding that he knew enough.

Actually, Dixon was surprised at how easily he'd accepted the idea of the Phantom's existence. Even before General O'Neill had spoken in his defence, he'd been intrigued at the very idea of Atlantis having its own masked vigilante, and the discovery that the Phantom had started out when he was a teenager from Earth with no prior knowledge of the Stargate program or the Ancients just made it all more impressive.

OK, so the Phantom had a leg-up from Elizabeth Weir through that bizarre time-travel paradox thing he'd heard so much about, but that didn't mean he hadn't come a long way however you looked at it.

_Maybe I'm just a bigger Batman fan than I thought_, Dixon mused, as he picked up another drink from the makeshift bar that had been established in this area, _but that guy _really _makes you admire him_.

"Colonel Dixon?" Norina asked, his new chief scientist walking up to him with a smile, wearing her new outfit of loose trousers and a long coat as opposed to her original floor-length dress. "Is everything well?"

"It's fine; just taking in the group," Dixon said, nodding reassuringly at Norina as he indicated the gathering around them. "I was just… you know, I'm not sure I've ever told you or your people how much we appreciate your willingness to adapt whatever plans you had for the _Orion _once we showed up."

"On the contrary, we're the ones who should be thanking you, colonel," Norina smiled back at him. "The Phantom helped us get the _Orion _back into working condition, but your own expedition has given us all we need to ensure that it can make a true difference in this galaxy, and we are proud to assist in that goal in any way we can."

"No hard feelings about not owning the ship in full?"

"We may have repaired it, but we always knew that we weren't experienced enough at conflict on this kind of scale to use it against the Wraith to make a real impact," Norina said dismissively. "Believe me, we're all grateful for your decision to take charge on that issue."

"So long as you always remember that your input is just as valued as anyone else's," Dixon countered.

"Always a good thing to keep in mind," a voice said from a nearby corridor.

"Pard-?" Dixon began, his eyes widening as he turned to look at the corridor and realised that the Phantom was standing there, positioned just to the side of the door so that he couldn't be seen by the rest of the room even as Dixon and Norina could see him clearly.

"_Phantom_?" Norina said, her voice low but excited as she looked at him. "You're here?"

"Always have been," the masked man smiled, as Dixon and Norina walked over to join him in the corridor. "I just… prefer to take a back seat for the moment now that people are starting to step up on their own."

"Really?" Dixon asked, confused about what John Sheppard was doing showing up to something like this in his Phantom outfit rather than his military uniform. "So… why are you even here?"

"Well," the masked man chuckled slightly, "let's just say it's… been a while since I went anywhere to do more than kill Wraith and keep people safe." He turned to look directly at Norina. "I just thought that, after everything you helped me with in terms of getting the _Orion _into working order, your people deserved to know that I can't guarantee I'll be around a lot, but you should know that I'm still here; you just… don't need me around on a regular basis."

"We owe you a great deal-"

"And I appreciate that, but my main reason for helping you was always to help you; you don't need to think of yourselves as _owing _me anything," John said reassuringly. "All I ask is that you continue doing what you can to help the people of Atlantis and the rest of this galaxy deal with the Wraith; I'll still be there to help out when I'm really needed, but I think this galaxy's reaching a point where I'm not needed full-time."

Norina looked uncertainly at the masked man for a moment, but finally smiled and nodded at him in understanding.

"Well… it's not like we didn't manage without you before…"

"And you're not losing me now; I'm just not stepping in as much as I used to," John said, smiling back at her before he turned to Dixon. "Keep it up with the _Orion_, Colonel Dixon; I expect great things from her."

"I'll do what I can," Dixon nodded in response, smiling slightly as the Phantom turned and vanished back into the darkened corridor behind him.

Nobody had ever been able to work out how the man did that, but these days it was just a neat trick and a useful edge if they had another incident like that time with the Genii and the storm; Dixon, for one, wasn't going to complain about Atlantis's military leader knowing things about the city that nobody else did.

He just hoped things reached the point where Norina and a few others could be told the truth about John's real history sooner rather than later…

* * *

AN: I know that this chapter was a bit short, but considering what happened in canon at this time, I mainly wrote it to assure everyone that the Taranians will be safe; Michael didn't have time to access all the data from the Atlantis database in this world and he'd be reluctant to target the Taranians anyway given their closer ties to Atlantis due to the _Orion_ (which isn't to say that he isn't still carrying out those experiments, just that his range of 'viable material' is more limited).

Anyway, next chapter we move to the new assault on the Asuran homeworld, which will set off a chain of events that culminate in a moment I'm sure everyone has been waiting for…


	13. First Strike

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

When the announcement came through, John didn't have time to apply his 'make-up'; even after expecting the ship for a while, on another level it was hard to adjust to the idea that the SGC could spare more ships for Pegasus rather than them relying on _Orion _and the occasional visit from _Daedalus_.

It was a strange thing to find unnerving, but the last few weeks had been the quietest time he could ever remember since he'd arrived in Pegasus. He was aware that the Wraith were still out there in the wider galaxy, but all of their allies had reported that there was no sign of approaching hive-ships, and there had been little contact with the Wraith during their more standard trips through the Stargate. He was aware that things had been busy back in the Milky Way galaxy, following the mass suicide of the Asgard and the subsequent final defeat of the Ori armies, but aside from it meaning that Earth could spare more resources to help Atlantis, the final defeat of the Ori didn't really impact his regular routine that much.

At the moment, it was almost pleasant to only have to worry about a few personal issues rather than bigger threats. Carson had reported that his new deputy chief of medicine, a Doctor Jennifer Keller, was having some trouble with the pressure of her new role, but he and Elizabeth had each assured her that they were comfortable with her staying where she was despite that. McKay was having trouble with his yearly performance reviews, protesting that he didn't really know most of the people who worked in the city by name, but Elizabeth had countered that if John was making the effort he certainly should (Even if John didn't find himself with much more to say than to confirm the high standards of everyone in the military division of the city.

Still, going over all the personnel files to make sure that there was nobody he needed to single out for particular attention had taken time, with the result that John had been in his quarters when he'd received the message that the _Apollo _had arrived ahead of schedule. Quickly finishing his current sentence, John saved his work and hurried to the briefing room after putting on his mask; he didn't want to waste time applying his make-up for someone who should already know what he looked like. By the time he reached the conference room, Elizabeth and McKay were already sitting around the table with two folders in front of them, along with an unfamiliar man with dark skin and a completely bald head, looking at John with a slight smile as he entered.

"John Sheppard, I presume?"

"The mask gives it away, right?" John said, shaking the other man's hand as he took the offered folder. "Sorry about not being here; end-of-year evaluations, you know…"

"_He _does those?" McKay looked at Elizabeth indignantly. "He's only been in charge a few months; shouldn't someone else do that?"

"He's been in the city before we were, Doctor; I think we can assume that John knows what his staff are capable of," Elizabeth said, shooting an apologetic glance at John before she turned back to the other man. "Well, Colonel Ellis, now that John's here, what's this briefing you wanted to talk to us about?"

"Ever since the human-form Replicators made a play for the city, we've had the _Daedalus_ make regular reconnaissance fly-bys of their home planet."

"Which we know," John noted as he sat down beside Elizabeth.

"Two months ago, it took these pictures," Ellis said, activating a projector to display a photograph of large, flat areas on what was some kind of planet surface.

"I'm sorry, what am I supposed to be looking at here?" Elizabeth asked, staring thoughtfully at the screen.

"Nothing."

"Eh?" John cut in, wondering if this was some kind of military psyche-out he hadn't learned about.

"This image," Ellis continued, the projector now showing the same area with arrows indicating objects that hadn't been there before, "was taken about three weeks ago in the very same location. They're building ships; a lot of them."

"And nobody told _us _about this earlier because…?" John asked, looking at Ellis with a pointed glare.

"We were making plans back on Earth," Ellis replied, countering John's glare with his own.

"Well, if they're coming for us, we should start making preparations to bolster the shield," McKay cut in. "I mean, we should-"

"They're not gonna get here," Ellis said firmly. "I'm here to inform you that in precisely twelve hours, the _Apollo_, in consort with your team, will launch a surgical strike on the Replicator planet."

"You'll blow up their ships?" John asked.

"That's right," Ellis confirmed.

"Just like that?" Elizabeth added.

"Just like that."

"How the hell do you plan on doing that?" McKay inquired.

"A set of Mark Nine tactical nukes housed in a custom-made weapons platform codenamed Horizon."

"OK… When you say 'set', how many are we talking here?" John inquired.

"The Horizon carries six warheads and four decoys," Ellis said, before looking over at McKay. "I'm gonna need you to do a final inspection before we-"

"Hold on; _six _nukes against Replicators?" John cut in. "I grant that I've only met the local ones, but I read the files when I was on Earth; can you really blow them up when they've got that whole 'self-replicating' thing going on?"

"The Milky Way ones were self-replicating, yes, but these ones aren't," Ellis clarified. "Their ships aren't built from nano-cells; they're constructed of real material that can be destroyed. Six will be more than enough for now."

"'For now'?" McKay repeated incredulously. "Look, isn't this a bit like poking a sleeping dragon? Why don't we just wait 'til Area 51 finishes the P.W.A. ?"

"Which one's that again?" Elizabeth asked before John had to ask it; this new job required him to keep so many acronyms straight it was easy to miss a few.

"Planetary Wide Anti-Replicator Weapons," McKay clarified before turning back to Ellis. "Look, the Asgard were capable of creating a satellite that could wipe out an entire Replicator planet. I mean, we've had some trouble making one of our own but-"

"Look, would I prefer taking out an entire planet at once?" Ellis began.

"OK, I think we should all be clear that it's the _Replicators _that are the problem; we're not here to blow up the damn _planet_ just because we can-" John cut in.

"_The point_," Ellis continued with a pointed glare at John, "is that this image is giving the IOA a lot of sleepless nights. The Replicators know the location of Earth and, with these new ships, have the means to get there; we can't just sit on our hands while the guys at Area 51 try to come up with a solution."

"…OK, I get that," John said, shaking his head in resignation.

"This mission's primary objective is to eliminate key military targets; we'll come back and finish once the new weapon is up and running," Ellis said, turning back to McKay. "Doctor, I'm gonna need you to start your inspections as soon as possible."

McKay had barely begun to stammer out his acknowledgement before Ellis had given the order to beam the Canadian scientist to the ship, leaving Ellis to pick up the photographs and leave the briefing room as though the issue of what to do next was already decided.

"Can you believe this?" Elizabeth asked, standing up to look at the photo still on the screen.

"I know," John said, getting up to study the image beside Elizabeth. "I'm all for taking out the Replicators, but diving in like this before we're completely ready…"

"You don't agree?"

"I'm… not entirely comfortable with their decision," John said, shrugging awkwardly at the city's leader after a moment's thought. "I get where the IOA are coming from, and I think we can safely say that those ships make it clear the Asurans are after more than just Atlantis, but attacking when we can see that they're not ready to do anything and we've just got to wait a bit longer to get something that can put them all down at once…"

"You feel that we'd be knocking down a hornet's nest with a broom when we just need to wait a week for the pesticide?"

"…Longer time frame, but the analogy sounds about right," John acknowledged with a brief shrug. "Granted, I was never one for gardening or pest control…"

"I'll try and have another word with Colonel Ellis to discuss this," Elizabeth said, smiling gratefully at John; he might not be a trained soldier in the same way as other members of the expedition, but he was developing a keen insight into the enemy in Pegasus that she knew for a fact SG-1 in particular had come to respect during their crash course with him.

She didn't want to use him as a reference in case certain parties in the IOA decided that this meant that John was proving to be a difficult military commander, but the knowledge that he agreed with her doubts made her feel better.

* * *

When he checked in on Elizabeth in her office a couple of hours later, she looked so frustrated that John briefly thought about leaving her until she'd cooled down, but reminded himself of all the times she'd managed to get him to open up when he hadn't realised he needed to; if she could do it for him, he could do it for her.

"What's up?" he asked, looking curiously at her as he walked into the office.

"Just…" Elizabeth began, before sighing in frustration. "Have you ever had one of those days when you feel like you're just here because people needed someone to sign everything?"

"What?"

"I tried to tell Colonel Ellis that using nuclear weapons would be an ineffectual first strike, but as far as he was concerned, the IOA don't think that we can waste time with pointless negotiations and that's that. I mean, he actually _told _me that I don't have the authority to tell him to stand down and basically stated that my input doesn't matter-!"

"It does to me," John noted, cursing himself as soon as the words were past his lips.

"I mean…" he said, shrugging uncomfortably as Elizabeth looked at him, "I get that some people back on Earth think you might not be the best choice for this role now that they know there's a war here, but seriously, you think I didn't get a few critics when I was… well, 'applying' for this job? You're never going to please everybody, but that doesn't mean you should doubt yourself?"

"I spoke to General O'Neill and Mr Woolsey, but they both stand by the IOA's decision even when I'm the one out here assessing the situation directly; every time there's a major problem, it seems like the military just wants to step in and assuming control…"

"If that was the case, I think we can both agree I wouldn't be here."

"Pardon?"

"I said it when the siege began, and I'll say it again; you are the _only _leader of Atlantis I would _ever _obey without question," John said firmly. "If people back on Earth don't think you should be here, I doubt they'd have let you pull all the strings needed to let me take over the military contingent here, to say nothing of everything you must have gone through to make my role here official."

"Well… General O'Neill and Mr Woolsey helped-"

"After you made the original suggestion; they might have been overruled by the naysayers back on Earth this time around, but you can't start doubting yourself because some people think you aren't doing the job _they'd _want you to do," John said firmly. "You have the faith of the right people, and that's all that should matter to you."

"Thanks," Elizabeth said, smiling gratefully at him before her smile faltered. "For what it's worth, McKay's confirmed that the weapons platform is viable and ready to be deployed."

"Doesn't mean you're happy about it, right?"

"I understand that we could probably never negotiate with machines that have been nurturing their grudge against the Ancients and us for millennia, but that doesn't change the fact that I feel that deploying nukes instead of a specific anti-Replicator weapon is a mistake."

"How about McKay?" John asked. "If he says the platform isn't ready-?"

"He's already confirmed that it is," Elizabeth cut in. "Zelenka thought about trying to say the platform wasn't ready, or maybe even make sure of it, but McKay just didn't feel comfortable going that far even if he disagrees with the situation."

"Ah," John shrugged. "That must be why Ellis requested Lorne head up to the _Apollo _earlier."

"Lorne?" Elizabeth noted in surprise.

"Something about wanting a trained professional there to provide an experienced perspective on the whole thing," John said. "Personally, I think they just didn't want me up there because I made my stance clear."

"Your 'stance'?"

"If you don't like a plan, I don't like a plan; Colonel Ellis might not be able to kick me out of Atlantis, but he could make sure I wasn't in a position to show that," John clarified.

"Right," Elizabeth smiled, grateful for John's show of solidarity.

It might not change the minds of anyone back on Earth, but knowing that John Sheppard had that kind of faith in her leadership despite their contrasting styles and experiences…

Elizabeth couldn't place why that made her feel so much better, but it did.


	14. Assault on Atlantis

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

AN: I apologise in advance that this chapter doesn't end this episode, but it felt like it would be too long if I included Atlantis taking off as well given my other plans for these events; hope you like the results anyway

Clash of the Phantoms

"So," Elizabeth said, looking contemplatively at Major Lorne as he stood in front of her and John in her office, "you're sure the ships were destroyed?"

"Believe me, they couldn't have survived what Horizon sent out against them," Lorne said firmly. "That explosion was… well, it was big."

"And the Replicators couldn't have done something about it?" John asked. "They _are _pretty fast…"

"Colonel Ellis considered that," Lorne replied. "We had opened the bomb bay doors while still in hyperspace and dropped them at pretty much the moment we got out of it; they wouldn't have had time to react to a blast like that, and that's before I ran a closer check. Zelenka said something about it being hard to get an accurate yield calculation at this distance, but McKay seemed fairly sure we had done all the damage we needed."

"That's good to know," John said, before looking probingly at Lorne. "And… did Ellis have anything to say about us?"

"Actually, the colonel had a few things to say about Doctor Weir's abilities as a leader in a military situation like this, but he just seemed to want to get a general feel for my thoughts on the situation rather than actually objecting to you two," Lorne clarified. "When I told him that I was completely satisfied with the two of you as leaders, he decided that it wasn't worth pressing the issue at the time."

"Really?" John looked at his official second-in-command with a smile. "Thanks, Major."

"No problem," Lorne nodded back. "The SGC isn't exactly a conventional military outpost by any stretch of the imagination, and that's when we have immediate access to anything we need back on Earth. In my book, that means we need an unconventional leader to deal with the situation out here; if the IOA don't like it, they should give us an alternative that we can be sure would actually work, instead of just complaining about you."

"We appreciate the support, Major Lorne," Elizabeth nodded, just as Chuck hurried into the conference room.

"Doctor Weir?" he said, looking anxiously at the city's leader. "You're going to want to see this; we've got a contact, just came out of hyperspace."

With a quick glance at Elizabeth, John got up and hurried from the conference room to the control room, looking anxiously at the data on the screen.

"Is it broadcasting IFF?" Elizabeth asked.

"No, ma'am," Chuck confirmed.

"Too small to be anything Wraith, but get the shield up just to be sure," John put in.

"Done," Chuck nodded, triggering the relevant controls before turning back to the screen. "Whatever it is, it's taking up a geosynchronous orbit above the city."

"Can we get the _Apollo _to check it out?" John asked.

"Tell Colonel Ellis to get right on it," Elizabeth noted, glancing at Chuck as he tapped a few controls on a nearby laptop.

"Think it's them?" Ronon asked, as he and Teyla walked into the control area, a grim expression on the former Runner's face.

"I'm learning to expect the worst," John said simply, even as the screen indicated the _Apollo _taking off to take a closer look at the new arrival.

"Apollo _to Atlantis_," Colonel Ellis reported at last. "_We have a visual on the object; it appears to be a satellite, but it has… well, there appears to be a Stargate in the centre of it_."

"Hold on; it's a satellite _and _a Stargate?" John asked. "Are you saying someone built a satellite around a Stargate and fired it off to us?"

"_Actually… since this Stargate only seems to have eight chevrons, I wouldn't be surprised if someone built it and the satellite at the same time_…"

"Built a Stargate…" John said, looking thoughtfully over at McKay as the Canadian scientist hurried into the control room. "I'm getting a very bad feeling about this…"

"The Replicators?"

"_It just activated_," Ellis' voice said before John could reply to the scientist's query. John was about to ask for more details when there was a loud series of explosions at the other end of the radio connection before it cut out.

"What happened?" John asked, glancing anxiously at the technician.

"_Apollo_'s still up there, but there's been a major energy surge from the satellite; it must have forced _Apollo _to back off," Chuck reported, his fingers flying over the board. "The satellite's turning around; it's firing… it looks like some kind of energy beam at the planet."

"Shield's up, right?" McKay asked.

"Yes-" Chuck began, just as the city shuddered when the beam made contact with the edge of the shield. As those in the control tower ran to see the source of that shudder, they took in the sight of a vast beam of red energy hurtling down from the sky, the city's shield rippling against the force being directed against it even as it held up to the barrage.

"It's a sustained beam," Chuck confirmed grimly.

"That is bad for a dozen different reasons," McKay noted grimly.

"_It's protected by a shield_," Ellis's voice called out over the radio. "_Give me some options, McKay_."

"The shield's taking its power from the beam," McKay

"Look, I registered a slight drop in output when you fired on it…"

"_Could I get a nuke past its shield_?"

"No, probably not," McKay said.

"I'll get down to the Chair and give it everything we've got," John said firmly, his gaze fixed on the beam. "Maybe that'll collapse the shield…"

"I said 'slight'," McKay said, before John could do more than turn towards the door of the control room. "As in point zero zero two percent."

"Ah," John noted.

"Not something we can rely on, then?" Lorne added.

"Quite frankly, I doubt _any _amount of firepower is gonna collapse it while that beam is active."

"_So what do we do_?" Ellis asked.

"We stand down and let me think, is what we do," McKay said as he headed for another console. "Just give me five minutes to get my bearings. I'll brief you."

"McKay, it's shooting at us," Ronon noted.

"Yes, and the shields are _holding_," McKay said firmly. "We've got plenty of time; just give me five minutes."

Exchanging anxious glances with Elizabeth, John noted that at least he wasn't the only one sceptical about that idea; if they were being attacked by something able to build Stargates, he had his doubts that even McKay could come up with a solution in five minutes.

For the moment, he was going to make sure that all of his own emergency measures for a direct attack on Atlantis were still available if he had to resort to them; the hyperspace-capable jumper had been kept in reserve in the underwater bays ever since he'd become the official military commander of the city, but there was nothing he could do about the power supply as they already had three ZPMs plugged into the city, and he couldn't be sure if _Apollo _had one of the ones he'd donated already or not…

* * *

"We're in trouble," McKay reported, as Ellis joined John and Elizabeth in Elizabeth's office once he'd been beamed through the shield.

"And it took you five minutes to work that out?" John asked.

"Look, the satellite is basically just a stripped-down ship," McKay explained. "There's a hyperdrive engine, a shield, and navigational systems. There's a small power source that was designed to take it to its intended target and power the shield until the Gate can be dialled. But once a wormhole has been established to whoever's on the dialling side, it fires a beam into their Stargate and it comes out on our side, allowing them to fire on us _and_ to power the satellite."

"Clever," John noted.

"Yes; as long as they can keep the beam powered from home, the weapon remains operational. Oh, and one fun added side bonus is that because their Stargate is in such close proximity to our planet, we can't dial our Stargate. We're stuck."

"But can't we… hold on…" John began, pausing mid-sentence as one of the SG-1 mission reports he'd read back on Earth came to him. "Didn't Anubis once try something similar to this on Earth's Stargate? I read a file where he found some Ancient weapon that sent a massive amount of energy into the 'gate so that it couldn't shut down until it blew up and took everything else with it?"

"Are you saying that bypassed the whole 'thirty-eight minute' rule I heard about how long we can maintain a wormhole?" Ellis asked. "I thought that wasn't possible?"

"Oh, it's possible, believe me; I was in the SGC when Anubis mounted that attack and I couldn't figure out _any _way of stopping it," McKay confirmed grimly. "We had to dump the Stargate in space and make some complicated deal with Russia to get back our original Stargate… God, they were annoying…"

"How do you get the power for something like that?" John asked. "Last I checked, it takes a lot of energy to run the Stargate normally, and I think if the Ancients left that kind of thing lying around we'd have seen it before…"

"Considering that you'd need either a black hole or an unlimited number of ZedPMs to do something like this, we can safely assume this is new," McKay said grimly.

"Well, at least that confirms it's the Replicators," John noted. "Who else could do that and build a Stargate?"

"Hopefully," McKay noted. "It's either that or we've just discovered another super-powerful enemy, so here's hoping it's just them."

"If this is anything like a normal Stargate, could we contact the dialling planet?" Elizabeth asked.

"Well…" McKay paused in thought for a moment. "I'd need to boost the signal considerably to get through the interference, but, uh, yes."

"See what you can do," Elizabeth nodded at the scientist.

"You want to _talk _to them?" Ellis asked, looking incredulously at Elizabeth as McKay left the room. "It's a waste of energy-"

"And trying to destroy a shield we have no idea how to destroy isn't?" John interjected firmly. "You can keep running your tests if you like, but we've already established that our available weaponry can't do anything to that shield, so apart from sitting around and twiddling our thumbs until we come up with a better plan, talking is all we've got right now, so we might as well use it."

"Precisely," Elizabeth nodded gratefully at him before fixing Ellis with a firm stare. "And before you get started on a massive debate about who's right or who's wrong in this situation, at the end of the day I'm responsible for the well-being of this city, and you don't have the authority to tell me to stand down, so with all due respect, I think I'll place my call."

Ellis clearly didn't like that turn of events, but as Elizabeth walked out to the control room, all the colonel could do was look at John in frustration while John shrugged nonchalantly back at him.

It might be a petty act, but considering that this man had basically been asking around to find out if John and Elizabeth were considered bad leaders by their people, John felt entitled to enjoy the notion that the man had misread the situation that badly.

As he returned to the control room to wait for further developments, occasionally checking the power controls to be sure that the shield was still holding against the barrage that it was being subjected to, John was relieved when McKay reported a response to his transmission through the orbiting Stargate. As Elizabeth waited in front of the communication screen, John moved to join her, but Elizabeth was clearly startled at the sight of the old man who responded to the transmission.

"Oberoth?" she said, John taking a moment to recognise the name as the 'leader' of the Replicators when they'd assumed they were just another Ancient city.

"_Doctor Weir_," the apparent old man responded.

"I must say, I'm surprised to see you," Elizabeth said, quickly collecting herself.

"_Each of us exists within the collective and can be replicated many times_," Oberoth replied.

"Ah," John noted, before privately dismissing it; in this situation, it might actually be enjoyable to have more than one chance to kick that arrogant bastard's ass.

"You need to disable your weapon immediately," Elizabeth responded, bringing the conversation directly to the topic at hand.

"_That is not possible._"

"We had no choice but to attack you," Elizabeth said, returning to her diplomatic roots. "You're building warships. They need to be neutralised."

"_And now, so do you_."

"That assault was just the tip of the spear," Elizabeth continued. "We were hoping it would bring you to your senses. If you don't stop this aggression, we will be forced to launch an all-out attack."

"_Really_?" Oberoth asked. "_Why have you waited_?"

"Because we were hoping that we could talk to you people and work out something that we'd all find agreeable rather than just blow you all up," John noted.

"The annihilation of your people is not our goal," Elizabeth continued, shooting John a look that he wasn't sure how to interpret. "Ideally, we would like a peace to exist between us, but we will not stand idly by while you build ships and weapons that can be used to destroy us."

"_Interesting_," Oberoth said in his usual cool tone. "_We feel the same way about you_."

John wished that he had some way to wipe that condescending grin off the old man/Replicator's face, but considering that Atlantis and Earth had been planning to attack the Arusan homeworld anyway, he didn't exactly have a moral high ground to stand on.

"Perhaps I should remind you every time we've met in battle, _our_ side has been clearly victorious," Elizabeth countered.

"Elizabeth," McKay cut in, "they're attempting to upload a virus on the comm bandwidth. I've been able to stop it for now but I'm not-"

"Shut it down," Elizabeth said, nodding at McKay to terminate the video link as the screen shifted to static. "Well, that went well."

"So," John asked, before McKay could voice his own frustration, "assuming that they can keep that beam going regardless of usual time limits, how long have we got until it penetrates the shield?"

"With our current ZPMs, assuming constant pressure… I'd give it a week at most," McKay said grimly.

"OK," John said, looking around the control room. "First priority is be ready to try the simple option in case this thing does shut down at the thirty-eight-minute mark; after that, I need options, like… shut this thing down at the source?"

"The _Apollo _isn't in any state to get into a battle right now-"

"I need options, not objections, _Colonel_," John said, turning to glare at Ellis. "We're in this mess because your superiors decided to start firing rather than wait; find me something we can actually _do _about this mess."

"Oh, now we're responsible for this?" Ellis countered, walking over to stand in front of John, the man once known as the Phantom suddenly wondering if Ellis would be this bold if he'd taken his make-up off to reveal his true face. "You know, you might have managed to pull some strings to get this job-"

"I got this 'job' because General O'Neill and the SGC agreed with the decision to trust my experience over my lack of official qualifications, Colonel," John countered. "If you have a problem with my decisions, put them to the IOA when you get back to Earth, but right now this is my outpost, my responsibility, and my enemy to beat, so stop trying to convince our team to turn on us and let me work out how the hell we're going to survive this mess, _comprende_?"

Maybe it wasn't professional, but that was the advantage of his position existing technically outside the conventional chain of command; he might not have an official rank, but in Atlantis, it had been made clear to the SGC that his word would be law, which meant that he had full authority to tell Ellis to get out of his face while he focused on saving the city he'd come to call home.

Looking at the anxious expression on Elizabeth's face, he just hoped that she wasn't going to start doubting her own role in the city if this kept up; the IOA might want her to act as a scapegoat for some of their worse decisions out here, and they may not have faith in her role as anything more than an administrator, but John would make it clear to anyone who would listen that he trusted Elizabeth above anyone else, and would cite these events as proof that her opinion had value in a crisis.

He just had to be careful he didn't let _that_ out of the bag…

* * *

A few hours later, staring up at the red beam now coming down at Atlantis through several tons of water, John wondered if he should feel nostalgic at the moment.

He might not have always felt comfortable living alone in Atlantis when he'd arrived, but there had been something cool about the concept of living in a sunken city created by an ancient civilisation. He'd taken to watching the fish on a few occasions when he'd known that particular shoals were passing by the tower- it had reached a point where sometimes he could only be sure what time of year it was on the planet based on what was swimming near Atlantis- but at the moment he didn't have anything to distract him from the bigger problem, the beam churning the water between the surface and the shield to such an extent that he doubted anything was going to pass the city now.

Submerging the city to use the water as additional protection had seemed like a good idea at the time, but even with all three ZPMs powering the submersion system to make it as efficient as possible, and as much as the residents had tried to appreciate the moment, it didn't change the fact that they were in trouble. Even with everything they'd done, going underwater had only brought them another couple of days at most, and John didn't want to run out these ZPMs any more than he had to; he might have a secret surplus, but those things didn't grow on trees.

John had been working on a little plan of his own, but he couldn't see how it would work unless they could take the beam out of the picture; right now, the city was the Asurans' priority, and he doubted that it would be easy to make them stop that beam even if he could convince them to go after another target.

So far, however, all he'd managed to do was make a weak joke comparing his recon team to the Fantastic Four that Teyla and Ronon didn't get, and he was running out of patience; no matter how much time they had, he hated being stuck in one place when there was a threat to stop.

"John?" Elizabeth asked, as she walked out to join him on the balcony. "Are you all right?"

"Well as you'd expect," John shrugged, looking back at her with a brief smile. "Just feeling stuck, I suppose."

"Feels like the old days?"

"Worse," John mused, indicating the marine landscape before them. "Back when I was here on my own, it was kind of cool to see some of the fish swimming around- I even worked out the best towers to watch some of the more regular migrations- but now we've got nothing to look at thanks to that beam stirring up the water, I can't work out what to do about this, and I don't even have the option of gating somewhere more interesting to think."

"That… must be frustrating," Elizabeth noted, looking thoughtfully at him. "I mean, I knew Atlantis was your home before we came here, but I guess I never really thought about how you spent your time… when you weren't killing Wraith, anyway."

"It had its ups and downs," John noted. "You can only exercise and train so often before you start feeling like you're just wearing yourself out when you can't actually compare your results to anything else. Managed to trade for some paper and pen equivalents to try writing and drawing at times, but… well, the results were poor."

"Just like my reputation back on Earth?"

"You're still here-"

"And I'm starting to wonder if I'll be here much longer, given how far the IOA went over my head with the attack that started this mess in the first place."

"…You don't think that's my fault?"

"Excuse me?" Elizabeth looked at him in surprise.

"The IOA jumping over you like that, I mean," John clarified. "It's just… well, you pulled a lot of strings to get me an official role here, and that can't have made some of the IOA very happy; could I-?"

"Don't," Elizabeth cut in, looking firmly at him. "You earned your role on this expedition with every drop of blood and sweat you've given to keep this galaxy as safe as one man could; you may not have been an official part of this expedition at the beginning, but I will _never _regret making sure that you were allowed to stay here."

"…Thanks," John finally nodded, not trusting himself to say any more as he looked out at the sea once again.

_God, I wish I could kiss her right now_…

"_We have something_!" McKay's voice suddenly yelled over the radio, cutting John's thoughts off before they could become any grimmer.


	15. Atlantis in Space

Disclaimer: I don't own 'Stargate Atlantis' or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by 'The Phantom of the Opera', although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Clash of the Phantoms

"We _fly _away?" Lorne looked sceptically at McKay.

"It's perfect!" the Canadian scientist grinned. "With all three ZedPMs still at a comfortable power level, all we need to do is get off the ocean, out of the atmosphere, and then get the hyperdrive working before that satellite has a chance to… plant a tracker on us or something!"

"And the reason we didn't think of this earlier is?" John noted.

"Well… moving the city for one attack seemed a bit much until every other option to deal with the satellite had been used up…" McKay said, shrugging awkwardly before his gaze hardened again. "But we _can _do this; the Ancients repaired several key systems when they took control of the city, and I reiterate the three ZedPMs we've got not! I just need a couple of hours to make sure everything's fully charged and ready to go before we launch, and then we can use a couple of drones to knock that satellite off-target long enough to enter hyperspace."

"That is important?" Teyla asked.

"Do _you _want to try and fly away while that thing's still able to shoot at us?"

"Good point," Satterfield acknowledged.

"And we have enough power for this?"

"If we were still on just one ZedPM, I'd say we need a boost, but with all three acting together, we're pretty much sorted," McKay confirmed. "Admittedly, it's a shame that we'll have to leave that drilling platform behind before we got a good look at it, but we can send a team back here once we've convinced the Replicators we've abandoned the place and find a Stargate that can be spared by another planet."

"Too bad we can't just call in _Orion_ for back-up," Ronon noted.

"Good idea, but unfortunately even the _Orion _would take too long to penetrate that shield, and that's assuming that it got back here on its own in time."

"I thought Lieutenant Satterfield and Doctor Zelenka were working on a means of establishing long-range communication with the _Orion_?" Teyla asked.

"We've made some progress in that area, but it won't work when the shield's up like this," Satterfield put in. "Regular functions can continue unimpaired, but the city's devoting too much power to the shield to transmit a signal that far."

"And it wouldn't work, anyway; the _Orion_'s nice, but it can't do anything that we couldn't try here," McKay put in.

"We appreciate that various alternatives have been considered and disregarded for good reasons at this point; this isn't the time to start second-guessing ourselves now that we have a clear plan," Elizabeth cut in, looking firmly around at her senior staff. "The question that matters most right now is simple; now that we have a plan, can we carry it out?"

"With the shield at full power and a couple of drones ready to fire at just the right moment to throw that beam off-target?" McKay nodded. "We can do this."

"Then get to work," Elizabeth said firmly.

As the scientist left for his lab while Elizabeth moved to make a broadcast to the city, John mused that at least he could be fairly sure that he didn't have anything to do for a while; it would give him time to run a couple more tests for his own little idea…

* * *

Sitting in her office as they prepared for their next step, Elizabeth had to admit that she was feeling good about their chances. She'd issued orders to the rest of the city to prepare for the activation of the city's stardrive, and everyone was moving anything that could be spared into the central tower to minimise the strain on their energy reserves while in-flight; McKay was confident that they would have sufficient power, but Elizabeth felt that it didn't hurt to be prepared. She'd even had a fairly civil conversation with Colonel Ellis before he'd returned to the _Apollo _with other non-essential personnel, during which he'd actually apologised on his own accord about his earlier attitude towards her, claiming that he was just used to being the one calling the shots.

She wasn't sure if she completely accepted that, but at least it seemed like nobody here was secretly planning to kick her out of Atlantis any more. She might have some doubts about her role, but if John had been watching her for three years by now, she liked to think that he would have established if she was doing a good job or not, given his own experience with Pegasus.

Glancing at her watch, she noted that John should be settling into position in the control chair to start the flight right now, which meant that it was time for her to return to the control room rather than just go over the papers in her office. Walking into the control room, she noted her staff doing over various pre-flight checks as they finalised the coding commands necessary to start Atlantis's stardrive. According to McKay, approximately thirty percent of their total power requirements for this flight would be needed just to get them off the ocean, but even with the satellite beam striking their shields, three ZPMs should be enough to get them out of the atmosphere, at which point John would knock the satellite off-target long enough for them to trigger the hyperdrive and get away.

It was the most complex bit of flying anyone had ever done in Earth's current history, but it was the best plan they had right now, and she had faith that John could pull it off.

"Are we ready?" she looked over at McKay as he stood over one of the primary consoles.

"Well…" McKay began before he trailed off and shrugged helplessly. "Here goes nothing."

It wasn't the most encouraging thing he could have said, but Elizabeth could see his train of thought well enough; this plan still had its risks, but they didn't have anything better they could try.

His mind fixed on the current goal, McKay activated some controls, and Elizabeth heard the sound from their first day in the city, as the failsafe mechanism activated and released the city to float back to the surface. She wondered if John was aware of the finer details of the city from his position in the control chair, or if he just knew that they were moving, but the question became academic as they breached the surface and the red beam illuminated the shield directly once again.

"We're on the surface," McKay called into his radio. "Fire up the stardrive!"

As soon as the command was issued, the city shook, and Elizabeth thought she saw water boiling at the edges of the pier out of the nearest window before it ascended up from the sea, accompanied by the same strange jolt in her stomach Elizabeth always felt when the plane she was in took off.

"That's it!" McKay grinned, his eyes wide as he looked up from the console with a broad grin. "We're flying!"

Even the red glow of the city shield couldn't mar this moment for Elizabeth, as she walked over to take in the nearest window with a satisfied smile.

This wasn't something she'd ever planned to do with her life, but the thought of commanding a flying city was still a concept that appealed to a childish part of her; the fact that they were about to evade a dangerous enemy just gave it a more practical reason…

"We're leaving the atmosphere!" she called out, activating her radio as she spoke to let John know what was happening.

"_On it_!" John replied, before she saw two drones leave the city and head towards the source of the beam that was still striking the shield. As the drones struck, the beam temporarily shifted position to aim away from the city, but Elizabeth could see it already turning back around towards them…

Then there was a sudden jolting sensation as the stars around them accelerated away, and the city was in the blue 'tunnel' of hyperspace, flying away from the planet that had been Atlantis's home for the last few thousand years towards its next destination.

_We did it_, Elizabeth thought, grinning at the sound of cheers behind her. _We beat the Replicators… we're safe…_

"_Elizabeth_?" John's voice cut in over the radio.

"Yes?" Elizabeth asked, quickly tapping her radio in response.

"_The hyperdrive can pretty much run on automatic at this point, so can we get everyone together right now_?" her military leader asked. "_I have something I'd like to run by you all_."

* * *

"OK," Lorne looked curiously at the man once known as the Phantom as the Atlantis senior staff gathered in the conference room once again, "we're on our way, so what's this meeting about?"

"Quite frankly," John said firmly, "now that we're en route, I have another idea I'd like to run by you."

"Pardon?" McKay looked sharply at John. "You had another idea-?"

"For dealing with the Replicators, but it would only work once we'd dealt with the satellite issue, and that was still a big 'maybe'," John clarified. "You know that hyperspace-capable jumper I used to intercept those Wraith hives during our last meeting with Michael?"

"Yeah… how did you make something like that anyway?"

"I found an old lab somewhere in the city that had been working on the project and used the notes put it together in my spare time," John explained. "It's not capable of intergalactic travel on its own- I had to latch onto the signature of the hives' engines and follow that to get the right boost this time around- but if we're in hyperspace along the route we planned, if we just drop out at a certain point, the jumper should be enough to get me to Asuras-"

"_Asuras_?" McKay and Elizabeth yelled simultaneously.

"You _want _to _go _to _Asuras_?" McKay said, looking at John as though he'd gone insane. "In a _jumper_? What are you going to do, try a kamikaze assault with a nuke?"

"I was thinking that it might be possible to access the Asuran mainframe and reactivate their original programming to eliminate the Wraith," John corrected the scientist, enjoying the brief stunned looks he received at that statement before he continued. "I didn't see any point in suggesting it as a solution when we were still under attack as the Asurans would probably prefer to finish the old job before getting on with the new one, but now that they don't know where we are, wouldn't the Asurans go for the easier target rather than waste time finding us?"

"That…" McKay began, before he paused and nodded thoughtfully. "Actually, that might work; if we can access the central data core and reactivate the command code to attack the Wraith, they _would _probably revert to their default programming…"

"I thought you were against attacking the Asurans?" Elizabeth asked.

"I was against attacking them when we couldn't wipe them out completely with one stroke," John clarified. "What I'm proposing is a surgical strike that should allow us to turn our newer adversary against our more long-term threat until we can finish the anti-Replicator weapons."

"That's… it could actually work," Satterfield noted. "I mean, it wouldn't work against the old Replicators because we never had access to their central node, but if the Asgard could use Reese to lure in the other Replicators back in the day, we could probably do _something _similar here."

"I could hide the attack code with a bunch of spam data and they might just think I was attempting to disrupt them with a virus," McKay nodded thoughtfully. "Ask them to find the final digit of pi, prove that P equals NP, things like that…"

He paused for a moment, lost in thought, before he shook his head. "No, it wouldn't work; if we're going to get in and out without being detected, we'll need access to the Replicators' nanite network in the first place."

"Ah," John said awkwardly. "Just cloaking the ship and getting in close isn't an option, then?"

"It would get us into the city, don't get me wrong, but as soon as we do anything to disrupt their systems, they'd know about it and intercept us, unless we had some way of diverting their attention away from us that we can access apart from via the central core."

"And we don't have that…" John groaned, lowering his head in frustration. "Damnit, I really thought I had something there…"

"And you do," McKay said, suddenly looking awkwardly at John. "We _do _have a means of accessing the nanite network…"

"We do?" John asked in surprise. "What is it?"

"Elizabeth."

"Excuse me?" John said, his tone shifting from hopeful to cold as he glared at the Canadian scientist.

"She still has the deactivated nanites that Niam tried to infect her with before we shut them down," McKay clarified, indicating the city's leader. "They're dormant right now, but if I can work out a program to reactivate them in a semi-dormant state so that they don't try and rewrite her body into one of them, we should be able to use her to distract the Replicators long enough for us to find where the central core is and reactivate the attack code-"

"_No_."

"Hey, this was your idea-"

"And I will repeat myself; _no_," John said firmly. "I am not taking Elizabeth into the heart of Replicator territory-"

"You don't have to; I'm going."

"Excuse me?" John looked sharply at her. "Elizabeth, this isn't some diplomatic mission-"

"And it's not like I've never been in danger before, John," Elizabeth noted grimly. "I was here when the Wraith attacked us at the end of the first year and when the Asurans tried to take over the city a few months ago; it's not my regular role, but I can do it."

"All I need you to do is basically provide an access port to the mainframe so that I can keep track of where the other Asurans are, and I can add a kill-switch that would allow me to shut them back down if any of them try to take control of _you _in return," McKay smiled. "We get in, get the code, and get back out; maybe we can even get a new ZedPM or two if the opportunity arises."

"I have my reserves-"

"And we can't always rely on those; it can't hurt to have one or two available if we need a boost on short notice," McKay added. "Look, I get that this probably isn't the way you _wanted _to put this plan into action, but it's the best way we've got right now, so can we just get to the Asurans and take it from there?"

Staring at the Canadian scientist in frustration for a moment, John finally sighed and glanced over at Elizabeth.

"If you're sure?" he said.

"I'm sure," Elizabeth nodded.

"Right," John said, standing up from the table. "Let's go before I change my mind."


End file.
